From karplus@bray.cse.ucsc.edu Mon May 6 11:16:04 2002 Date: Mon, 6 May 2002 11:15:48 -0700 From: Kevin Karplus To: compbio@soe.ucsc.edu CC: karplus@soe.ucsc.edu CASP5 registration just opened. I'll register us as SAM-T99 (CAFASP) SAM-T02-human (CASP only) when the SAM-T02 server is up, we can register it as SAM-T02-server (CAFASP) From mailer@bialko.llnl.gov Mon May 6 11:16:19 2002 Date: Mon, 6 May 2002 11:16:13 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: CASP5 Predictor Registration X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK CASP5: Predictor Registration ============================= Thank you for registering your interest in the Fifth Critical Assessment of Techniques for Protein Structure Prediction Experiment (CASP5). For your records, a summary of your registration is printed below. Please save and print out this file for your records. Keep a note of your Predictor Registration Code. You will need this to update your registration details. REMEMBER: To submit predictions you will need your "Group Leader" registration code. Predictor Registration Code = 4069-6308-1312 1. Name Kevin Karplus 2. Name of Institution University of California, Santa Cruz 3. Mailing address Street: Computer Engineering City: Santa Cruz State: CA Zip: 95064 Country: USA 4. Telephone 1-832-459-4250 5. Fax - 6. Email karplus@soe.ucsc.edu 7. Registration type group leader 8. Group Name (e.g. Smith-John) SAM-T02-human 9. Likelyhood of submitting predictions under different categories of the experiment Comparative Modelling: Likely Fold Recognition ('threading'): Certain Ab initio: Likely 10. Source of information about experiment previous participation From mailer@bialko.llnl.gov Mon May 6 11:37:18 2002 Date: Mon, 6 May 2002 11:37:12 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: CASP5 Predictor Registration (SERVER: SAM-T99) X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK CASP5: Predictor Registration (SERVER) ====================================== Thank you for registering your interest in the Fifth Critical Assessment of Techniques for Protein Structure Prediction Experiment (CASP5). For your records, a summary of your registration is printed below. Please save and print out this file for your records. Keep a note of your Predictor Registration Code. You will need this to update your registration details. REMEMBER: To submit predictions you will need your "Group Leader" registration code. After this registration is completed, you must also register your server data at the CAFASP-3 metaserver site at http://cafasp.bioinfo.pl/. Only servers that have registered both at the Prediction Center and at the CAFASP-3 metaserver will participate in CAFASP. Predictor Registration Code = 6269-7633-6117 1. Name Server Registration: Kevin Karplus, http://www.soe.ucsc.edu/research/compbio/HMM-apps/T99-query.html 2. Name of Institution University of California, Santa Cruz 3. Mailing address Street: Computer Engineering City: Santa Cruz State: CA Zip: 95064 Country: USA 4. Telephone 1-831-459-4250 5. Fax - 6. Email karplus@soe.ucsc.edu 7. Registration type group leader 8. Group Name (e.g. Smith-John) SAM-T99 9. Likelyhood of submitting predictions under different categories of the experiment Comparative Modelling: Likely Fold Recognition ('threading'): Certain Ab initio: Likely 10. Source of information about experiment CAFASP (Server Registration) From casp5@bialko.llnl.gov Mon May 6 11:52:32 2002 Date: Mon, 6 May 2002 11:52:25 -0700 (PDT) From: CASP5 To: karplus@cse.ucsc.edu Subject: CASP5 announcement X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK ----------------------------------------------------------------------- Dear CASP5 Registrant: Attached is a public announcement of the CASP5 experiment. We would appreciate your help in disseminating the information as widely as possible. So please forward the message to any colleagues or relevant email lists. Thanks, CASP5 organizers. ---------------------------------------------------------------------- Announcing the Fifth Community Wide ------------------------------------ Experiment on the Critical Assessment of ---------------------------------------- Techniques for Protein Structure Prediction ------------------------------------------- (CASP5) ------- Introduction ------------ CASP experiments aim at establishing the current state of the art in protein structure prediction, identifying what progress has been made, and highlighting where future effort may be most productively focused. There have been four previous experiments, in 1994, 1996, 1998 and 2000. Full details of these may be found at the CASP web site, http://PredictionCenter.llnl.gov/, and in the special issues of the journal PROTEINS: 23(5), 1995; Suppl 1, 1997, Suppl 3, 1999 and Suppl 5, 2001. In CASP4, 163 prediction groups from all around the world took part. We now announce the fifth experiment. As before, the goal is to obtain an in-depth and objective assessment of our current abilities and inabilities in this area. To this end, participants will predict as much as possible about a set of soon to be known structures. These will be true predictions, not 'post-dictions' made on already known structures. Full details will be available at http://predictioncenter.llnl.gov/casp5. The experiment will begin in May 2002, when the first prediction targets will be made available. The prediction season will run through August. There will be a meeting at the Asilomar Conference Center in California December 1 - 5th, to discuss the results. In more detail: =============== Scope of CASP5 and Related Experiments -------------------------------------- As in earlier CASPs, all types of methods for predicting protein structure will be considered, ranging from comparative modeling through fold recognition and 'new fold' prediction. Most emphasis will be on tertiary structure prediction but secondary structure and contact prediction methods will also be included. A new category, prediction of disordered regions in proteins, will be introduced. In addition, there will be additional activities included in CASP5, which will extend the scope substantially: CAFASP3: In the era of genome sequencing, rapid protein structure modeling methods have a critical role to play. This experiment, led by Dani Fischer, will evaluate automatic methods of predicting protein structure, using the CASP targets. All targets will be processed through prediction servers that register for the experiment. Models will be evaluated by the same numerical criteria as used for CASP5, as well as the CAFASP criteria, and a session at the CASP5 meeting will compare performance through the servers with that obtained when full human participation is allowed. Further details of this experiment may be found at: http://www.cs.bgu.ac.il/~dfischer/CAFASP3/ Large scaling benchmarking: It is hoped that the results of well run benchmarking experiments such as EVA and LIVEBENCH will also be included in the CASP meeting and publications. Ten Most Wanted: Results of the community effort to produce useful models of ten proteins of particular biological or medical interest will also be discussed at the meeting. Experiment ---------- The broad goals of the CASP5 experiment are to address the following questions about the current state of the art in protein structure prediction: 1. Are the models produced similar to the corresponding experimental structure? 2. Is the mapping of the target sequence onto the proposed structure (i.e. the alignment) correct? 3. Have similar structures that a model can be based on been identified? 4. Are the details of the models correct? 5. Has there been progress from the earlier CASPs? 6. What methods are most effective? 7. Where can future effort be most productively focused? In addition, CASP5 will focus particularly on areas of prediction that previous CASPs have shown to be current bottlenecks to progress. Suggested problem areas are: 1. Alignment of a sequence onto a template fold. 2. Model refinement - improving the accuracy of an initial model. 3. Accurately modeling regions of insertion and deletion relative to a template structure. 4. Improved fold recognition, particularly for analogous, analogous/new fold targets. 5. Improved New Fold methods. 6. Bold new methods aimed at removing one of the current bottlenecks to progress. To facilitate progress in some of these areas, partly built models will provided where necessary, for example, correct alignment as a starting point for loop building, and full approximate models as a starting point for refinement. The MD community is encouraged to participate, making use of these starting points. The set of problem areas may be revised, following discussion with the consultancy groups. Participants are advised to check for revisions. Prediction Targets ------------------ For the experiment to succeed, it is essential that we obtain the help of the experimental community. As in previous CASPs, we will invite protein crystallographers and NMR spectroscopists to provide details of structures they expect to have made public before 1st October 2002, using the target submission form available at http://PredictionCenter.llnl.gov/casp5. Prediction targets will be made available through the web site. All targets will be assigned an expiry date, and predictions must be received and accepted before that expiration date. Participation ------------- Participation is open to all. Intending CASP predictors must register at the web site: http://PredictionCenter.llnl.gov/casp5 Those interested in receiving mailings concerning progress of the experiment may also register as 'observers'. CAFASP predictors must register at that web site. Participation in both experiments (initial submission of server generated models to CAFASP and subsequent submission of models based on human interaction to CASP) is encouraged. Note that separate registrations are required for CASP and CAFASP participation. Assessment of Predictions ------------------------- As in previous CASPs, independent assessors will evaluate the predictions. There will be three assessors, representing expertise in the comparative modeling, fold recognition and new fold prediction areas. Assessors will be provided with the results of numerical evaluation of the predictions, and will judge the results primarily on that basis. They will be asked to focus particularly on the effectiveness of different methods. As CASP has grown, the work of the assessors has become more and more demanding. To help them with their task, predictors and target submitters will be asked to assist in the evaluation of models. Numerical evaluation criteria will as far as possible be very similar to those used in CASP4, although the assessors may be permitted to introduce some additional ones. Appropriate members of the prediction community will be asked to develop methods of assessing the statistical significance of performance ranking, a controversial area in the past. Release of Results ------------------ 1. All CASP predictions and evaluations will be made available through this web site, shortly before the meeting. 2. The proceedings of the meeting will be published. In recent CASPs, the large number of predictors together with the limited number of published predictor papers has been one of the main causes of excessive focus on winners and losers. To combat that, the mix of papers in the special issue will altered. There will not be a predefined number of 'winner' group papers. Instead, papers that focus on problem areas and solutions will be included. 3. In a further change to increase recognition of the contributions of more predictors, a new web site will be developed, allowing all participants to report their work if they wish, and encouraging vigorous discussion of the results. Meeting ------- A meeting will be held 1-5 December, 2002 at Asilomar, California, USA to evaluate the results of the prediction experiment. The meeting will be limited to about 200 participants and precedence will be given to active predictors. It is hoped that some financial assistance will be available for the more successful predictors. It is expected that the format of the meeting will be changed from previous CASPs, concentrating more on progress in problem areas, rather than the best performers in each section, irrespective of whether there has been a significant change since last time. Organizing Committee -------------------- John Moult CARB, UMBI, USA jmoult@tunc.org Krzysztof Fidelis Lawrence Livermore National Laboratory, USA fidelis@llnl.gov Adam Zemla Lawrence Livermore National Laboratory, USA adamz@llnl.gov Tim Hubbard Sanger Centre, Hinxton, UK th@sanger.ac.uk Support ------- The organizers gratefully acknowledge support for the CASP5 experiment from the NIH and the Department of Energy. Additional industrial support is being sought. More Information ---------------- Further details will be available at the web site (http://PredictionCenter.llnl.gov/casp5) Please address any questions or queries to casp5@PredictionCenter.llnl.gov From mailer@bialko.llnl.gov Wed May 15 09:50:09 2002 Date: Wed, 15 May 2002 09:50:02 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: CASP5 Predictor Registration (SERVER: SAM-T02-server) X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK CASP5: Predictor Registration (SERVER) ====================================== Thank you for registering your interest in the Fifth Critical Assessment of Techniques for Protein Structure Prediction Experiment (CASP5). For your records, a summary of your registration is printed below. Please save and print out this file for your records. Keep a note of your Predictor Registration Code. You will need this to update your registration details. REMEMBER: To submit predictions you will need your "Group Leader" registration code. After this registration is completed, you must also register your server data at the CAFASP-3 metaserver site at http://cafasp.bioinfo.pl/. Only servers that have registered both at the Prediction Center and at the CAFASP-3 metaserver will participate in CAFASP. Predictor Registration Code = 5035-2079-5263 1. Name Server Registration: Kevin Karplus, http://www.soe.ucsc.edu/research/compbio/HMM-apps/T02-query.html 2. Name of Institution University of California, Santa Cruz 3. Mailing address Street: Computer Engineering City: Santa Cruz State: CA Zip: 95064 Country: USA 4. Telephone 1-831-459-4250 5. Fax 1-831-459-4829 6. Email karplus@soe.ucsc.edu 7. Registration type group leader 8. Group Name (e.g. Smith-John) SAM-T02-server 9. Likelyhood of submitting predictions under different categories of the experiment Comparative Modelling: Likely Fold Recognition ('threading'): Certain Ab initio: Likely 10. Source of information about experiment CAFASP (Server Registration) From karplus@bark.cse.ucsc.edu Wed May 15 10:10:50 2002 Date: Wed, 15 May 2002 10:10:49 -0700 From: Kevin Karplus To: karplus@soe.ucsc.edu Subject: copy of mail to adamz I accidentally registered the one too many times---please remove the following registration, leaving 3 predictors registered for me: SAM-T99-server SAM-T02-server SAM-T02-human CASP5: Predictor Registration Update ==================================== You registration details for the Fifth Critical Assessment of Techniques for Protein Structure Prediction Experiment (CASP5) have now been updated. For your records, a summary of your registration is printed below. Please save and print out this file for your records. Predictor Registration Code = 6009-1972-5717 1. Name Kevin Karplus 2. Name of Institution University of California, Santa Cruz 3. Mailing address Street: Computer Engineering City: Santa Cruz State: CA Zip: 95064 Country: USA 4. Telephone 1-831-459-4250 5. Fax 1-831-459-4829 6. Email karplus@cse.ucsc.edu 7. Registration type group leader 8. Group Name (e.g. Smith-John) error---remove-this-entry 9. Likelyhood of submitting predictions under different categories of the experiment Comparative Modelling: Likely Fold Recognition ('threading'): Certain Ab initio: Likely 10. Source of information about experiment past participation From adamz@llnl.gov Wed May 15 10:22:54 2002 MIME-Version: 1.0 Sender: adamz@bialko.llnl.gov Date: Wed, 15 May 2002 10:22:47 -0700 From: Adam ZEMLA Organization: Lawrence Livermore National Laboratory X-Accept-Language: en To: Kevin Karplus Subject: Re: [mailer@bialko.llnl.gov: CASP5 Predictor Registration (UPDATE)] Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Thank you for your message. Adam Kevin Karplus wrote: > > I accidentally registered the one too many times---please remove the > following registration, leaving 3 predictors registered for me: > SAM-T99-server > SAM-T02-server > SAM-T02-human > > CASP5: Predictor Registration Update > ==================================== > > You registration details for the Fifth Critical Assessment of Techniques > for Protein Structure Prediction Experiment (CASP5) have now been updated. > > For your records, a summary of your registration is printed below. > Please save and print out this file for your records. > > Predictor Registration Code = 6009-1972-5717 > > 1. Name > Kevin Karplus > 2. Name of Institution > University of California, Santa Cruz > 3. Mailing address > Street: Computer Engineering > City: Santa Cruz > State: CA > Zip: 95064 > Country: USA > 4. Telephone > 1-831-459-4250 > 5. Fax > 1-831-459-4829 > 6. Email > karplus@cse.ucsc.edu > 7. Registration type > group leader > 8. Group Name (e.g. Smith-John) > error---remove-this-entry > 9. Likelyhood of submitting predictions under different categories of the experiment > Comparative Modelling: Likely > Fold Recognition ('threading'): Certain > Ab initio: Likely > 10. Source of information about experiment > past participation -- *********************************************************************** Adam Zemla, Ph.D. | E-mail: adamz@llnl.gov Biology and Biotechnology Research Program | Phone: (925) 423-5571 Lawrence Livermore National Laboratory, L-448 | Fax: (925) 422-2282 7000 East Ave., Livermore, CA 94550, USA | Bldg: 3751, Room: 109 *********************************************************************** From dfischer@cs.bgu.ac.il Sun May 19 16:24:11 2002 From: Daniel Fischer Date: Mon, 20 May 2002 02:24:04 +0300 (IDT) To: karplus@soe.ucsc.edu X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Dear CAFASP3 server-developer, Your server(s) have been coupled to the CAFASP meta-server. The servers information is now listed in http://www.cs.bgu.ac.il/~dfischer/CAFASP3/servers.html. Please let me know if the data listed is not correct. The first targets will probably begin to appear soon, so have your servers ready. For those servers that have already been registered in casp (as servers), we list in the table the name given at the registration. For those of you who haven't yet registered your servers at casp, the table shows "Not Registered", so, please register as soon as possible. The casp registration will serve to identify each prediction in CASP. All the servers' predictions will be sent by the CAFASP meta-server to the prediction center using this id. Good prediction session! From karplus@bray.cse.ucsc.edu Mon May 20 10:07:20 2002 Date: Mon, 20 May 2002 10:07:13 -0700 From: Kevin Karplus To: dfischer@cs.bgu.ac.il CC: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu In-reply-to: <200205192324.CAA15117@lace.cs.bgu.ac.il> (message from Daniel Fischer on Mon, 20 May 2002 02:24:04 +0300 (IDT)) Dani, You have the test site registered for SAM-T02, not the final URL that I used for the official registration. The interface should be the same, just the URL is different. We'll be using the test site for experimentation, and would rather not have the CAFASP entries going to it. The official URL is http://www.ucsc.soe.edu/research/compbio/HMM-apps/T02-query.html Thanks. Kevin From dfischer@cs.bgu.ac.il Mon May 20 10:09:37 2002 MIME-Version: 1.0 X-Authentication-Warning: silver.cs.bgu.ac.il: dfischer owned process doing -bs Date: Mon, 20 May 2002 20:08:22 +0300 (IDT) From: Daniel Fischer X-Sender: dfischer@silver To: Kevin Karplus cc: leszek@bioinfo.pl, rachelk@soe.ucsc.edu Subject: Re: your mail In-Reply-To: <200205201707.g4KH7DI26135@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Kevin, Ok, changed. > You have the test site registered for SAM-T02, not the final URL that > I used for the official registration.The interface should be the > same, just the URL is different.We'll be using the test site for > experimentation, and would rather not have the CAFASP entries going to > it. > > The official URL is > http://www.ucsc.soe.edu/research/compbio/HMM-apps/T02-query.html > > Thanks. > Kevin > From rachelk@grunt.cse.ucsc.edu Mon May 20 11:26:41 2002 MIME-Version: 1.0 From: Rachel Karchin Content-Type: text/plain; charset=us-ascii Date: Mon, 20 May 2002 11:26:29 -0700 To: Daniel Fischer , leszek@bioinfo.pl CC: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu Subject: SAM_T02 unavailable In-Reply-To: X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Daniel and Leszek: Just wanted to let you know that SAM_T02 will be unavailable for the next several days, due to emergency downtime of the main file server used by our group. I will send you email as soon as our file system comes back online. Please do not submit any targets to SAM_T02 in the meantime. -- rk ------------------------------------------------------------------------- Rachel Karchin bioinformatics Ph.D. candidate Office phone: (831) 459-5431 http://www.cse.ucsc.edu/~rachelk email: rachelk@cse.ucsc.edu From dfischer@cs.bgu.ac.il Mon May 20 14:33:52 2002 MIME-Version: 1.0 X-Authentication-Warning: lace.cs.bgu.ac.il: dfischer owned process doing -bs Date: Tue, 21 May 2002 00:33:45 +0300 (IDT) From: Daniel Fischer X-Sender: dfischer@lace To: Rachel Karchin cc: leszek@bioinfo.pl, karplus@soe.ucsc.edu Subject: Re: SAM_T02 unavailable In-Reply-To: <15593.16341.323857.465539@grunt.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Rachel, I am sorry to hear about the downtime in such a critical time. The first target is likely to be out very soon, hopefully not too late for your server to be available before the 48 hour deadline. Please let Leszek know as soon you are ready to receive queries, so his meta-server sends it. > Daniel and Leszek: > > Just wanted to let you know that SAM_T02 will be unavailable > for the next several days, due to emergency downtime of the > main file server used by our group. > > I will send you email as soon as our file system comes back > online. > > Please do not submit any targets to SAM_T02 in the meantime. > > -- rk > > ------------------------------------------------------------------------- > Rachel Karchin > bioinformatics Ph.D. candidate > Office phone: (831) 459-5431 > http://www.cse.ucsc.edu/~rachelk > email: rachelk@cse.ucsc.edu > From casp5@bialko.llnl.gov Tue May 21 14:58:32 2002 Date: Tue, 21 May 2002 14:58:25 -0700 (PDT") From: CASP5 To: karplus@soe.ucsc.edu Subject: CASP5: First TARGET X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear Predictor, This message is to inform you that the first target (T0129) is included in the CASP5 target database at http://PredictionCenter.llnl.gov/casp5/Casp5.html Please check "target list". CASP5 organizers *********************************************************************** Adam Zemla, Ph.D. | E-mail: adamz@llnl.gov Biology and Biotechnology Research Program | Phone: (925) 423-5571 Lawrence Livermore National Laboratory, L-448 | Fax: (925) 422-2133 7000 East Ave., Livermore, CA 94550, USA | Bldg: 3751, Room: 109 *********************************************************************** From apache@cyborg.bioinfo.pl Wed May 22 02:19:49 2002 From: leszek@bioinfo.pl To: karplus@soe.ucsc.edu, dfischer@cs.bgu.ac.il, leszek@bioinfo.pl, rost@columbia.edu Cc: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu, stu@soe.ucsc.edu Subject: Re: question about update Date: Wed, 22 May 2002 11:19:46 +0200 (CEST) X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Great, I sent the target. Please let me know if You notice any problem (I will send it again). Yours, Leszek ---- Original Message ---- From: Kevin Karplus Date: Wed 5/22/02 2:27 To: dfischer@cs.bgu.ac.il, leszek@bioinfo.pl, rost@columbia.edu Cc: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu, stu@soe.ucsc.edu Subject: Re: question about update It looks like the SAM-T99 and SAM-T02 servers are back up now. Please resubmit the first target, and let us know if there are any problems. We're still tracking down contamination from the failing file server, and may not have fixed everything that it broke. Kevin Karplus From karplus@bray.cse.ucsc.edu Wed May 22 09:48:02 2002 Date: Wed, 22 May 2002 09:47:45 -0700 From: Kevin Karplus To: leszek@bioinfo.pl CC: dfischer@cs.bgu.ac.il, rost@columbia.edu, rachelk@soe.ucsc.edu, stu@soe.ucsc.edu, karplus@soe.ucsc.edu In-reply-to: <20020522091946.4D9811CD913@cyborg.bioinfo.pl> (leszek@bioinfo.pl) Subject: Re: question about update I saw that the CAFASP site had gotten the SAM-T99 and SAM-T02 alignments, but for the secondary structure had only gotten the SAM-T99 prediction, and not the SAM-T02 predictions. The SAM-T02 predictions are on the web site at http://www.soe.ucsc.edu/research/compbio/SAM_T02/results/target02-query-1022059067-2517/ fp7296.t2k.stride-ebghtl fp7296.t2k.dssp-ebghstl (Those two files are the CASP format, there is also a tab-separated RDB format giving the full probability vectors and a FASTA-formatted .seq file.) Is there something different we need to do in order to get the secondary structure predictions included in the CAFASP meta server? From dfischer@cs.bgu.ac.il Wed May 22 11:06:00 2002 MIME-Version: 1.0 X-Authentication-Warning: lace.cs.bgu.ac.il: dfischer owned process doing -bs Date: Wed, 22 May 2002 21:05:52 +0300 (IDT) From: Daniel Fischer X-Sender: dfischer@lace To: Leszek Rychlewski cc: Kevin Karplus , rost@columbia.edu, rachelk@soe.ucsc.edu, stu@soe.ucsc.edu Subject: Re: question about update In-Reply-To: <3CEBCDF5.FCECC02D@bioinfo.pl> Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Kevin, Leszek, Because Burkhard is the person responsible for the ss predictions in cafasp, what you propose should be okayed by him first. Of course there is no harm in keeping the info now, but it will be up to Burk. what to do with it. D ------------------ Dr. Daniel Fischer Bioinformatics Dept. of Computer Science Ben Gurion University, Beer-Sheva 84015, Israel Tel +972-8-6472714 e-mail: dfischer@cs.bgu.ac.il Fax +972-8-6477650 or 6477648 http://www.cs.bgu.ac.il/~dfischer On Wed, 22 May 2002, Leszek Rychlewski wrote: > The secondary structure will not be evaluated and collected by us, but by Burkhard. Still it would > be convenient to send it to me and I would leave a copy here and send one to Burkhard. If You can > send the secondary structure automatically in a separate mail with a a priori known subject I could > handle this. (Actually I could also parse the body of the mail looking for "PFRMAT SS", so all I > need is the automated sending to the provided email). > > Yours, > > Leszek > > > Kevin Karplus wrote: > > > I saw that the CAFASP site had gotten the SAM-T99 and SAM-T02 > > alignments, but for the secondary structure had only gotten the > > SAM-T99 prediction, and not the SAM-T02 predictions. > > > > The SAM-T02 predictions are on the web site at > > http://www.soe.ucsc.edu/research/compbio/SAM_T02/results/target02-query-1022059067-2517/ > > fp7296.t2k.stride-ebghtl > > fp7296.t2k.dssp-ebghstl > > > > (Those two files are the CASP format, there is also a tab-separated > > RDB format giving the full probability vectors and a FASTA-formatted > > .seq file.) > > > > Is there something different we need to do in order to get the > > secondary structure predictions included in the CAFASP meta server? > > -- > Bioinformatics Laboratory, BioInfoBank > ul. Limanowskiego 24A, 60-744 Poznan, Poland > Tel: +48-61 865 3520 Fax: +48-61 864 3350 http://bioinfo.pl > > > From leszek@bioinfo.pl Wed May 22 09:57:30 2002 MIME-Version: 1.0 Sender: tytus@cyborg.bioinfo.pl Date: Wed, 22 May 2002 18:57:25 +0200 From: Leszek Rychlewski X-Accept-Language: en To: Kevin Karplus Cc: dfischer@cs.bgu.ac.il, rost@columbia.edu, rachelk@soe.ucsc.edu, stu@soe.ucsc.edu Subject: Re: question about update Content-Type: multipart/alternative; boundary="------------1C514E8B44EA21610314FC6D" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --------------1C514E8B44EA21610314FC6D Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The secondary structure will not be evaluated and collected by us, but by Burkhard. Still it would be convenient to send it to me and I would leave a copy here and send one to Burkhard. If You can send the secondary structure automatically in a separate mail with a a priori known subject I could handle this. (Actually I could also parse the body of the mail looking for "PFRMAT SS", so all I need is the automated sending to the provided email). Yours, Leszek Kevin Karplus wrote: > I saw that the CAFASP site had gotten the SAM-T99 and SAM-T02 > alignments, but for the secondary structure had only gotten the > SAM-T99 prediction, and not the SAM-T02 predictions. > > The SAM-T02 predictions are on the web site at > http://www.soe.ucsc.edu/research/compbio/SAM_T02/results/target02-query-1022059067-2517/ > fp7296.t2k.stride-ebghtl > fp7296.t2k.dssp-ebghstl > > (Those two files are the CASP format, there is also a tab-separated > RDB format giving the full probability vectors and a FASTA-formatted > .seq file.) > > Is there something different we need to do in order to get the > secondary structure predictions included in the CAFASP meta server? -- Bioinformatics Laboratory, BioInfoBank ul. Limanowskiego 24A, 60-744 Poznan, Poland Tel: +48-61 865 3520 Fax: +48-61 864 3350 http://bioinfo.pl --------------1C514E8B44EA21610314FC6D Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit The secondary structure will not be evaluated and collected by us, but by Burkhard. Still it would be convenient to send it to me and I would leave a copy here and send one to Burkhard. If You can send the secondary structure automatically in a separate mail with a a priori known subject I could handle this. (Actually I could also parse the body of the mail looking for "PFRMAT SS", so all I need is the automated sending to the provided email).

Yours,

Leszek
 

Kevin Karplus wrote:

I saw that the CAFASP site had gotten the SAM-T99 and SAM-T02
alignments, but for the secondary structure had only gotten the
SAM-T99 prediction, and not the SAM-T02 predictions.

The SAM-T02 predictions are on the web site at
        http://www.soe.ucsc.edu/research/compbio/SAM_T02/results/target02-query-1022059067-2517/
        fp7296.t2k.stride-ebghtl
        fp7296.t2k.dssp-ebghstl

(Those two files are the CASP format, there is also a tab-separated
RDB format giving the full probability vectors and a FASTA-formatted
.seq file.)

Is there something different we need to do in order to get the
secondary structure predictions included in the CAFASP meta server?

-- 
Bioinformatics Laboratory, BioInfoBank
ul. Limanowskiego 24A, 60-744 Poznan, Poland
Tel: +48-61 865 3520 Fax: +48-61 864 3350 http://bioinfo.pl
  --------------1C514E8B44EA21610314FC6D-- From karplus@bray.cse.ucsc.edu Wed May 22 14:56:41 2002 Date: Wed, 22 May 2002 14:56:35 -0700 From: Kevin Karplus To: leszek@bioinfo.pl Cc: dfischer@cs.bgu.ac.il, rost@columbia.edu, rachelk@soe.ucsc.edu, karplus@soe.ucsc.edu Subject: SAM-T02 makes TWO secondary structure predictions The SAM-T02 server makes two (sometimes rather different) secondary structure prediction. I noticed that you had put up the stride-ebghtl prediction, but not the dssp-ebghstl prediction on the CAFASP page. The two predictions do, in fact, differ a fair amount especially in the region around residues 110-122. I'd like for both predictors to be included in the evaluation. From dfischer@cs.bgu.ac.il Wed May 22 15:03:19 2002 MIME-Version: 1.0 X-Authentication-Warning: lace.cs.bgu.ac.il: dfischer owned process doing -bs Date: Thu, 23 May 2002 01:03:14 +0300 (IDT) From: Daniel Fischer X-Sender: dfischer@lace To: Kevin Karplus cc: leszek@bioinfo.pl, rost@columbia.edu, rachelk@soe.ucsc.edu Subject: Re: SAM-T02 makes TWO secondary structure predictions In-Reply-To: <200205222156.g4MLuZ013076@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Kevin, If you want two methods to be evaluated separately, the best is that you use separate names for each, but again, as this is ss, ALL issues concerning ss servers will be dealt by Burkhard only, and whatever he decides is ok with us! So please, be in contact with Burkhard and finallize all details about your methods and ss-servers with him only. Thx D ------------------ Dr. Daniel Fischer Bioinformatics Dept. of Computer Science Ben Gurion University, Beer-Sheva 84015, Israel Tel +972-8-6472714 e-mail: dfischer@cs.bgu.ac.il Fax +972-8-6477650 or 6477648 http://www.cs.bgu.ac.il/~dfischer On Wed, 22 May 2002, Kevin Karplus wrote: > > The SAM-T02 server makes two (sometimes rather different) secondary > structure prediction.I noticed that you had put up the stride-ebghtl > prediction, but not the dssp-ebghstl prediction on the CAFASP page. > The two predictions do, in fact, differ a fair amount especially in > the region around residues 110-122.I'd like for both predictors to > be included in the evaluation. > From karplus@bray.cse.ucsc.edu Wed May 22 15:13:41 2002 Date: Wed, 22 May 2002 15:13:35 -0700 From: Kevin Karplus To: dfischer@cs.bgu.ac.il CC: leszek@bioinfo.pl, rost@columbia.edu, rachelk@soe.ucsc.edu, karplus@soe.ucsc.edu In-reply-to: (message from Daniel Fischer on Thu, 23 May 2002 01:03:14 +0300 (IDT)) Subject: Re: SAM-T02 makes TWO secondary structure predictions I have been copying Burkhard on all the messages, but have not heard anything from him about what (if anything) he needs me to do to get the 2ry structure server properly evaluated. If you just need two names for the two secondary- outputs of the server, you could use sam-t02-stride sam-t02-dssp (We prefer sam-t02-stride to target02, which the current bioinfo.pl/Meta page is calling the secondary structure output). From dfischer@cs.bgu.ac.il Wed May 22 15:19:50 2002 MIME-Version: 1.0 X-Authentication-Warning: lace.cs.bgu.ac.il: dfischer owned process doing -bs Date: Thu, 23 May 2002 01:19:40 +0300 (IDT) From: Daniel Fischer X-Sender: dfischer@lace To: Kevin Karplus cc: leszek@bioinfo.pl, rost@columbia.edu, rachelk@soe.ucsc.edu Subject: Re: SAM-T02 makes TWO secondary structure predictions In-Reply-To: <200205222213.g4MMDZ413101@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Kevin, Maybe he is out of town; I am sure you will hear from him when he sees your emails. > I have been copying Burkhard on all the messages, but have not heard > anything from him about what (if anything) he needs me to do to get > the 2ry structure server properly evaluated. As said before, ss servers are handled by him, so about the names, this is something you have to work out with him. Sorry I can not be of more help; me and Leszek are doing only the HM/FR/AI servers. D > > If you just need two names for the two secondary- outputs of the > server, you could use > sam-t02-stride > sam-t02-dssp > (We prefer sam-t02-stride to target02, which the current bioinfo.pl/Meta page > is calling the secondary structure output). > From leszek@bioinfo.pl Thu May 23 07:43:48 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Kevin Karplus" , Cc: , Subject: RE: SAM-T02 makes TWO secondary structure predictions Date: Thu, 23 May 2002 16:44:12 +0200 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 In-Reply-To: <200205222213.g4MMDZ413101@bray.cse.ucsc.edu> X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear Kevin, I have changed the names. I can only include the 2d results if they are mailed each in a separate mail with the subject sam-t02-dssp and sam-t02-stride respectively. there is no difference in the files themselves. Yours, Leszek > -----Original Message----- > From: Kevin Karplus [mailto:karplus@soe.ucsc.edu] > Sent: Thursday, May 23, 2002 12:14 AM > To: dfischer@cs.bgu.ac.il > Cc: leszek@bioinfo.pl; rost@columbia.edu; rachelk@soe.ucsc.edu; > karplus@soe.ucsc.edu > Subject: Re: SAM-T02 makes TWO secondary structure predictions > > > > I have been copying Burkhard on all the messages, but have not heard > anything from him about what (if anything) he needs me to do to get > the 2ry structure server properly evaluated. > > If you just need two names for the two secondary- outputs of the > server, you could use > sam-t02-stride > sam-t02-dssp > (We prefer sam-t02-stride to target02, which the current > bioinfo.pl/Meta page > is calling the secondary structure output). > From rachelk@grunt.cse.ucsc.edu Thu May 23 08:56:02 2002 MIME-Version: 1.0 From: Rachel Karchin Content-Type: text/plain; charset=us-ascii Date: Thu, 23 May 2002 08:55:54 -0700 To: "Leszek Rychlewski" CC: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu Subject: RE: SAM-T02 makes TWO secondary structure predictions In-Reply-To: X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK For now, I will have the server send three emails when caspresults=on -- current email with the top five models in AL format -- sam-t02-dssp email -- sam-t02-stride email I can have this ready in a couple of hours. -- rk Leszek Rychlewski writes: > I have changed the names. > I can only include the 2d results if they are mailed each in a separate mail > with the subject sam-t02-dssp and sam-t02-stride respectively. there is no > difference in the files themselves. ------------------------------------------------------------------------- Rachel Karchin bioinformatics Ph.D. candidate Office phone: (831) 459-5431 http://www.cse.ucsc.edu/~rachelk email: rachelk@cse.ucsc.edu From leszek@bioinfo.pl Thu May 23 08:59:33 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Rachel Karchin" Cc: Subject: RE: SAM-T02 makes TWO secondary structure predictions Date: Thu, 23 May 2002 17:59:53 +0200 Content-Type: text/plain; charset="Windows-1252" X-Priority: 3 (Normal) X-MSMail-Priority: Normal Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 In-Reply-To: <15597.4362.979689.357815@grunt.cse.ucsc.edu> X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Perfect, I will test it after You send me an ok. Yours, Leszek > -----Original Message----- > From: Rachel Karchin [mailto:rachelk@soe.ucsc.edu] > Sent: Thursday, May 23, 2002 5:56 PM > To: Leszek Rychlewski > Cc: karplus@soe.ucsc.edu; rachelk@soe.ucsc.edu > Subject: RE: SAM-T02 makes TWO secondary structure predictions > > > For now, I will have the server send three emails when > caspresults=on > > -- current email with the top five models in AL format > -- sam-t02-dssp email > -- sam-t02-stride email > > I can have this ready in a couple of hours. > > -- rk > > Leszek Rychlewski writes: > > I have changed the names. > > I can only include the 2d results if they are mailed each in a > separate mail > > with the subject sam-t02-dssp and sam-t02-stride respectively. > there is no > > difference in the files themselves. > > ------------------------------------------------------------------------- > Rachel Karchin > bioinformatics Ph.D. candidate > Office phone: (831) 459-5431 > http://www.cse.ucsc.edu/~rachelk > email: rachelk@cse.ucsc.edu > From rachelk@grunt.cse.ucsc.edu Thu May 23 12:24:54 2002 MIME-Version: 1.0 From: Rachel Karchin Content-Type: text/plain; charset=us-ascii Date: Thu, 23 May 2002 12:24:48 -0700 To: "Leszek Rychlewski" CC: karplus@soe.ucsc.edu Subject: RE: SAM-T02 makes TWO secondary structure predictions In-Reply-To: X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Leszek Rychlewski writes: > Perfect, > > I will test it after You send me an ok. > > Yours, > > Leszek > Hi Leszek: Please go ahead and test SAM_T02 now. Let me know if you have any problems receiving the emails with the secondary structure predictions. -- rk ------------------------------------------------------------------------- Rachel Karchin bioinformatics Ph.D. candidate Office phone: (831) 459-5431 http://www.cse.ucsc.edu/~rachelk email: rachelk@cse.ucsc.edu From leszek@bioinfo.pl Thu May 23 12:52:48 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Rachel Karchin" Cc: Subject: RE: SAM-T02 makes TWO secondary structure predictions Date: Thu, 23 May 2002 21:53:14 +0200 Content-Type: text/plain; charset="Windows-1252" X-Priority: 3 (Normal) X-MSMail-Priority: Normal Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 In-Reply-To: <15597.16896.782525.206080@grunt.cse.ucsc.edu> X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Thanks, I just sent a request. The results will be at http://bioinfo.pl/meta/target.pl?id=7287 Yours, Leszek > -----Original Message----- > From: Rachel Karchin [mailto:rachelk@soe.ucsc.edu] > Sent: Thursday, May 23, 2002 9:25 PM > To: Leszek Rychlewski > Cc: karplus@soe.ucsc.edu > Subject: RE: SAM-T02 makes TWO secondary structure predictions > > > Leszek Rychlewski writes: > > Perfect, > > > > I will test it after You send me an ok. > > > > Yours, > > > > Leszek > > > > Hi Leszek: > > Please go ahead and test SAM_T02 now. > > Let me know if you have any problems receiving > the emails with the secondary structure predictions. > > -- rk > > ------------------------------------------------------------------------- > Rachel Karchin > bioinformatics Ph.D. candidate > Office phone: (831) 459-5431 > http://www.cse.ucsc.edu/~rachelk > email: rachelk@cse.ucsc.edu > From leszek@bioinfo.pl Thu May 23 13:32:36 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Rachel Karchin" Cc: Subject: RE: SAM-T02 makes TWO secondary structure predictions Date: Thu, 23 May 2002 22:33:02 +0200 Content-Type: text/plain; charset="Windows-1252" X-Priority: 3 (Normal) X-MSMail-Priority: Normal Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 In-Reply-To: <15597.16896.782525.206080@grunt.cse.ucsc.edu> X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Done, http://bioinfo.pl/Meta/target.pl?id=7287 Great, Leszek > -----Original Message----- > From: Rachel Karchin [mailto:rachelk@soe.ucsc.edu] > Sent: Thursday, May 23, 2002 9:25 PM > To: Leszek Rychlewski > Cc: karplus@soe.ucsc.edu > Subject: RE: SAM-T02 makes TWO secondary structure predictions > > > Leszek Rychlewski writes: > > Perfect, > > > > I will test it after You send me an ok. > > > > Yours, > > > > Leszek > > > > Hi Leszek: > > Please go ahead and test SAM_T02 now. > > Let me know if you have any problems receiving > the emails with the secondary structure predictions. > > -- rk > > ------------------------------------------------------------------------- > Rachel Karchin > bioinformatics Ph.D. candidate > Office phone: (831) 459-5431 > http://www.cse.ucsc.edu/~rachelk > email: rachelk@cse.ucsc.edu > From rost@columbia.edu Fri May 24 06:15:04 2002 MIME-Version: 1.0 Date: Fri, 24 May 2002 13:15:23 +0200 From: Burkhard Rost Reply-To: rost@columbia.edu Organization: Columbia University X-Accept-Language: en To: Kevin Karplus CC: "Eyrich,Volker" Subject: Re: SAM-T02 2ry structure predictor Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK dear kevin: ok, looking forward to that; my guess: will do worse ... let us see. b Kevin Karplus wrote: > > Burkhard, > > We have registered 2 servers for 2ry structure prediction in CASP5. > One is the SAM-T99 server that you have been testing already in EVA. > The other is a new one (similar methods, just retrained) that is part > of the new SAM-T02 server. > > The SAM-T02 server is at > http://www.soe.ucsc.edu/research/compbio/HMM-apps/T02.query > (I think I have that URL right---the file server that it lives on is > dead today, so I can't check. We hope to have the file server > resurrected by tomorrow.) > > The new server provides 2 different 2ry structure predictions---one > trained on STRIDE classification, one on DSSP classification. > We'd like to have both checked in EVA, since we are interested in > knowning how much of the difference between servers is due to the > difference between what "correct" answers they were trained on. > > We may add another predictor over the summer---I'll let you know if we do. > If we do, it'll be another file output from the same server, so that a > single submission will get all the predictions. > > Kevin Karplus -- -------------------------------------------------------------- Burkhard Rost CUBIC, Columbia University tel +1-212-305 3773 Dept Biochemistry & Mol Biophysics fax +1-212-305 7932 630 West, 168 Street, BB 217 New York, N.Y. 10032 Mail: rost@columbia.edu WWW: http://www.columbia.edu/~rost/ http://cubic.bioc.columbia.edu/ http://www.c2b2.columbia.edu/ From rost@columbia.edu Fri May 24 06:15:36 2002 MIME-Version: 1.0 Date: Fri, 24 May 2002 13:54:49 +0200 From: Burkhard Rost Reply-To: rost@columbia.edu Organization: Columbia University X-Accept-Language: en To: "Eyrich,Volker" , "Karplus,Kevin" Subject: [Fwd: Re: question about update] Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK volker: could you add? kevin: please put volker into your list ... b -------- Original Message -------- Subject: Re: question about update Date: Wed, 22 May 2002 09:47:45 -0700 From: Kevin Karplus To: leszek@bioinfo.pl CC: dfischer@cs.bgu.ac.il, rost@columbia.edu, rachelk@soe.ucsc.edu,stu@soe.ucsc.edu, karplus@soe.ucsc.edu References: <20020522091946.4D9811CD913@cyborg.bioinfo.pl> I saw that the CAFASP site had gotten the SAM-T99 and SAM-T02 alignments, but for the secondary structure had only gotten the SAM-T99 prediction, and not the SAM-T02 predictions. The SAM-T02 predictions are on the web site at http://www.soe.ucsc.edu/research/compbio/SAM_T02/results/target02-query-1022059067-2517/ fp7296.t2k.stride-ebghtl fp7296.t2k.dssp-ebghstl (Those two files are the CASP format, there is also a tab-separated RDB format giving the full probability vectors and a FASTA-formatted .seq file.) Is there something different we need to do in order to get the secondary structure predictions included in the CAFASP meta server? From rost@columbia.edu Fri May 24 06:15:43 2002 MIME-Version: 1.0 Date: Fri, 24 May 2002 13:59:54 +0200 From: Burkhard Rost Reply-To: rost@columbia.edu Organization: Columbia University X-Accept-Language: en To: Daniel Fischer , "Karplus,Kevin" , "Eyrich,Volker" , "Rychlewski,Leszek" Subject: Re: question about update Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK kevin: no problem; just subscribe as a different server, assumed that you did that already, didn't you? b Daniel Fischer wrote: > > Kevin, Leszek, > > Because Burkhard is the person responsible for the ss predictions > in cafasp, what you propose should be okayed by him first. Of course > there is no harm in keeping the info now, but it will be up > to Burk. what to do with it. > > D > > ------------------ > Dr. Daniel Fischer > Bioinformatics > Dept. of Computer Science > Ben Gurion University, Beer-Sheva 84015, Israel > Tel +972-8-6472714 > e-mail: dfischer@cs.bgu.ac.il > Fax +972-8-6477650 or 6477648 > http://www.cs.bgu.ac.il/~dfischer > > On Wed, 22 May 2002, Leszek Rychlewski wrote: > > > The secondary structure will not be evaluated and collected by us, but by Burkhard. Still it would > > be convenient to send it to me and I would leave a copy here and send one to Burkhard. If You can > > send the secondary structure automatically in a separate mail with a a priori known subject I could > > handle this. (Actually I could also parse the body of the mail looking for "PFRMAT SS", so all I > > need is the automated sending to the provided email). > > > > Yours, > > > > Leszek > > > > > > Kevin Karplus wrote: > > > > > I saw that the CAFASP site had gotten the SAM-T99 and SAM-T02 > > > alignments, but for the secondary structure had only gotten the > > > SAM-T99 prediction, and not the SAM-T02 predictions. > > > > > > The SAM-T02 predictions are on the web site at > > > http://www.soe.ucsc.edu/research/compbio/SAM_T02/results/target02-query-1022059067-2517/ > > > fp7296.t2k.stride-ebghtl > > > fp7296.t2k.dssp-ebghstl > > > > > > (Those two files are the CASP format, there is also a tab-separated > > > RDB format giving the full probability vectors and a FASTA-formatted > > > .seq file.) > > > > > > Is there something different we need to do in order to get the > > > secondary structure predictions included in the CAFASP meta server? > > > > -- > > Bioinformatics Laboratory, BioInfoBank > > ul. Limanowskiego 24A, 60-744 Poznan, Poland > > Tel: +48-61 865 3520 Fax: +48-61 864 3350 http://bioinfo.pl > > > > > > -- -------------------------------------------------------------- Burkhard Rost CUBIC, Columbia University tel +1-212-305 3773 Dept Biochemistry & Mol Biophysics fax +1-212-305 7932 630 West, 168 Street, BB 217 New York, N.Y. 10032 Mail: rost@columbia.edu WWW: http://www.columbia.edu/~rost/ http://cubic.bioc.columbia.edu/ http://www.c2b2.columbia.edu/ From karplus@bray.cse.ucsc.edu Fri May 24 10:09:36 2002 Date: Fri, 24 May 2002 10:09:32 -0700 From: Kevin Karplus To: rost@columbia.edu CC: dfischer@cs.bgu.ac.il, volker@chem.columbia.edu, leszek@sdsc.edu, karplus@soe.ucsc.edu In-reply-to: <3CEE2B3B.7358BEB9@columbia.edu> (message from Burkhard Rost on Fri, 24 May 2002 13:59:54 +0200) Subject: Re: question about update I have registered 3 times with CASP5 and twice with CAFASP SAM-T99 (CASP and CAFASP, fold-recognition and 2ry) SAM-T02-server (CASP and CAFASP, fold-recognition and 2 2ry) SAM-T02-human (CASP only) I have only subscribed the SAM-T02 server once. It provides a fold-recognition output and two 2ry structure prediction outputs. I was worried that trying to register it twice would result in two submissions to the same server. Currently, the server e-mails the fold-recogntion results back and they are incorporated into the CAFASP meta-server. Please tell me what to do. Should I register the SAM-T02 server 3 times? SAM-T02-server fold-recognition SAM-T02-server-dssp dssp-trained 2ry output SAM-T02-server-stride stride-trained 2ry output Twice? SAM-T02-server fold-recognition and stride-trained 2ry output SAM-T02-server-dssp dssp-trained 2ry output Once? SAM-T02-server fold-recognition and both 2ry predictors (The SAM-T99 server doesn't cause any problems, because it only provides on 2ry prediction.) From dfischer@cs.bgu.ac.il Fri May 24 10:53:10 2002 MIME-Version: 1.0 X-Authentication-Warning: silver.cs.bgu.ac.il: dfischer owned process doing -bs Date: Fri, 24 May 2002 20:51:22 +0300 (IDT) From: Daniel Fischer X-Sender: dfischer@silver To: Kevin Karplus cc: rost@columbia.edu, volker@chem.columbia.edu, leszek@sdsc.edu Subject: Re: question about update In-Reply-To: <200205241709.g4OH9W717185@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK I suggest 3 times, each for each method that you want evaluated. ------------------ Dr. Daniel Fischer Bioinformatics Dept. of Computer Science Ben Gurion University, Beer-Sheva 84015, Israel Tel +972-8-6472714 e-mail: dfischer@cs.bgu.ac.il Fax +972-8-6477650 or 6477648 http://www.cs.bgu.ac.il/~dfischer On Fri, 24 May 2002, Kevin Karplus wrote: > > I have registered 3 times with CASP5 and twice with CAFASP > SAM-T99 (CASP and CAFASP, fold-recognition and 2ry) > SAM-T02-server(CASP and CAFASP, fold-recognition and 2 2ry) > SAM-T02-human (CASP only) > > I have only subscribed the SAM-T02 server once.It provides a > fold-recognition output and two 2ry structure prediction outputs. > I was worried that trying to register it twice would result in two > submissions to the same server. > > Currently, the server e-mails the fold-recogntion results back and > they are incorporated into the CAFASP meta-server. > > Please tell me what to do.Should I register the SAM-T02 server 3 times? > SAM-T02-server fold-recognition > SAM-T02-server-dssp dssp-trained 2ry output > SAM-T02-server-stride stride-trained 2ryoutput > > Twice? > SAM-T02-server fold-recognition and stride-trained 2ry output > SAM-T02-server-dssp dssp-trained 2ry output > > Once? > SAM-T02-server fold-recognition and both 2ry predictors > > (The SAM-T99 server doesn't cause any problems, because it only > provides on 2ry prediction.) > From karplus@bray.cse.ucsc.edu Fri May 24 11:06:01 2002 Date: Fri, 24 May 2002 11:05:59 -0700 From: Kevin Karplus To: rachelk@soe.ucsc.edu CC: karplus@soe.ucsc.edu Subject: there will be THREE different predictor codes for CAFASP The CAFASP organizers have asked use to separate our different predictions to have "groups". There will be THREE different predictor codes for CAFASP: SAM-T02-server 5035-2079-5263 SAM-T02-server-dssp 2491-6940-1261 SAM-T02-server-stride 5144-8387-2760 Of course, we don't want to attach these code to any of the files---that is the job of the CAFASP organizers. From karplus@bray.cse.ucsc.edu Fri May 24 11:09:02 2002 Date: Fri, 24 May 2002 11:08:53 -0700 From: Kevin Karplus To: dfischer@cs.bgu.ac.il CC: rost@columbia.edu, volker@chem.columbia.edu, leszek@sdsc.edu, karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu In-reply-to: (message from Daniel Fischer on Fri, 24 May 2002 20:51:22 +0300 (IDT)) Subject: Re: question about update OK, I've now registered the SAM-T02 server 3 times: SAM-T02-server for the fold-recognition results SAM-T02-server-dssp for the dssp-trained 2ry prediction results SAM-T02-server-stride for the stride-trained 2ry prediction results I assume that there is no problem in your associating the correct name to the different results from the server. Let me know if anything else needs to be done. Kevin Karplus From leszek@bioinfo.pl Mon May 27 15:01:28 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Livebench@Bioinfo. Pl" Subject: first target completed Date: Tue, 28 May 2002 00:02:00 +0200 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 (Normal) X-MSMail-Priority: Normal Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear CAFASP participants. The first deadline expired. We have sent the first set of models to CASP. Each model can be viewed at http://bioinfo.pl/cafasp/3/targets/T0129/ (for target T0129, others will be added to T0130 etc.). The submitted model files have the names serverfilename.modelnumber.format. For historical reasons some server have strange serverfilenames (foldfit = 3DPSSM, burnham = FFAS), sorry about that. For server which generate genuine AL results two models were submitted. A translated TS model and an original AL model afterwards. The AL model should overwrite the TS model if no problems were detected. Otherwise the TS translation is submitted for safety. For servers, which do provide TS models or no AL models the original TS or a translation (respectively) was sent. Please verify if You like the models :-) CASP crew should notify You if they find errors in the models. A general problem with the translation into pdb (TS) format is that we align Your template sequence with our PDB files, disregarding the numbering You provide, because some servers don't provide any numbering or because of potential (frequent) differences in our and Your numbering. Sending original AL or TS models is thus safer for us. Translated model should be checked. A common problem can occur in cases where the your template sequence is LLLAKKK and our template sequence is for example LLLAAKKK (we don't know which A You mean). In general this affects the models very rarely, so I don't think we need to worry about this. Nevertheless You should check the translation if You find the time. Kind regards, Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl From leszek@bioinfo.pl Wed May 29 10:24:38 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Livebench@Bioinfo. Pl" Subject: CAFASP Date: Wed, 29 May 2002 11:56:55 +0200 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear all, You might have received few confirmation messages from CASP. Some models had errors. Please let us work on this first. Yours, Leszek From leszek@bioinfo.pl Wed May 29 10:57:43 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Livebench@Bioinfo. Pl" Subject: CAFASP Date: Wed, 29 May 2002 12:35:37 +0200 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear all 3 types of errors were observed: 1) parent chain mismatches, this can be fixed by us / CASP by removing the parent record (setting it to N/A) 2) some servers miss the TER record, I will try to fix this 3) expected problems with the AL format, this we will not fix. You can try it if You want => I will prepare the next set of models and send it again. Please wait for the next CASP messages and ignore if You want the previous ones. Yours, Leszek From leszek@bioinfo.pl Thu May 30 13:01:48 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Livebench@Bioinfo. Pl" Subject: CAFASP Date: Thu, 30 May 2002 22:02:09 +0200 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 (Normal) X-MSMail-Priority: Normal Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear All, This facility can tell You, which of Your models are accepted in CASP (and what format was used): http://predictioncenter.llnl.gov/casp5/models/casp5-models.html If You had sent predictions for T0129, 5 models should be there. As expected there were many problems with the AL format. Unexpectedly there were also problems with the TS format. For some reason CASP wants us to provide a parent if one was used for the TS models. The argue that they want to be able to tell whether a correct template was picked (???). I sent a new batch of models replacing PARENT records with 'PARENT N/A' to pass this filter. I don't know what they will do with this. They also don't know yet if they will accept this or not. Anyway, please be prepared for more error messages for target T0129. Please remember that the CAFASP evaluation is not affected by the CASP evaluation. Yours, Leszek PS: to explain the procedure again for people (servers) which reply with a AL format I send two models, our translation into TS (should be most likely accepted) and the original AL model, which if accepted will overwrite the TS model. As a result You can get 2 error messages per model (there are 5 models per target). If You get only one error message it means that the other format was probably accepted. Please check the model viewer (the link above). From casp5@bialko.llnl.gov Wed Jun 5 11:23:12 2002 Date: Wed, 5 Jun 2002 11:23:07 -0700 (PDT) From: CASP5 To: karplus@soe.ucsc.edu Subject: CASP5: New TARGET X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear CASP5 Predictor, This message is to inform you that a new target: T0131 is included in the CASP5 target database at http://PredictionCenter.llnl.gov/casp5/Casp5.html Please check "target list". CASP5 organizers From dfischer@cs.bgu.ac.il Wed Jun 5 16:09:48 2002 From: Daniel Fischer Date: Thu, 6 Jun 2002 02:09:41 +0300 (IDT) To: livebench@bioinfo.pl X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Dear CAFASP participant, This message is to clarify the CASP-CAFASP interaction process. In CAFASP, the collected server results are automatically translated into a standard pdb-like format. It is this translation that will be used for the CAFASP evaluation. For CAFASP, we only have one requirement: the meta-server has to know how to parse your server's output. For those servers not producing pdb-like output, Leszek has made his best efforts to translate the servers' output into this pdb-like format. In addition to CAFASP's evaluation, the server models will also be evaluated in CASP, along with the models submitted by human-casp participants. This CASP evaluation is independent of the CAFASP evaluation. In CAFASP2, we required that server developers submit their servers' predictions directly to CASP. To make the process more automatic, and to reduce the load on predictors, in CAFASP3, the server models (in the pdb-like format plus the casp required records) are automatically sent to the CASP's prediction center, where they need to pass strict formatting requirements. The translated models are available at: http://bioinfo.pl/cafasp/3/targets/T0XXX with the suffix TS or AL (with the author record not shown). If a server model is accepted, then the developer receives an acceptance message. If a model has casp formatting errors, then the developer receives an error message. You should have received such messages for your server models of T0129 and T0130. Server developers should correct the formatting errors and resubmit to the prediction center directly, as indicated in the message they receive. Please notice the following: 1. It is the developer's responsibility to resubmit to the prediction center the "corrected" rejected models. 2. The resubmission should be made directly to the prediction center. The CAFASP organizers (and Leszek in particular) will NOT be involved in this error correcting process; we only transfer the CAFASP models to CASP. We are not responsible for casp's prediction center. Please do not send to us any messages about your rejected models: this is something that needs to be resolved between each developer and the prediction center. If you have any questions or comments about the acceptance of your models at the prediction center, please contact them at: casp5@PredictionCenter.llnl.gov. Only in those cases where you believe that the meta-server has not parsed your server's output correctly, you should contact Leszek. 3. Warnings about C-alpha only models can be ignored. 4. Typical errors are missing chain specification in the PARENT record. CAFASP does not require a PARENT record, but CASP does. In these cases you could either include the correct chain, or use N/A. 5. The CASP organizers have promised us to try to help resolve the formatting problems with developers, so if you have problems "correcting" your models (and these are not due to an incorrect parsing of the meta-server), please contact the CASP team at casp5@PredictionCenter.llnl.gov. 6. Fortunately, the vast majority of models from T0129 and T0130 where either accepted, or had missing chain errors in the PARENT record, which are easily corrected. Thus, it appears that all the process will be smooth for most cases. 7. The models of T0129 were submitted twice. Please ignore the first messages you received last week. 8. If you have questions about the above procedure, do not hesitate to write! Good luck in CAFASP! Dani From casp5@bialko.llnl.gov Tue Jun 11 09:01:09 2002 Date: Tue, 11 Jun 2002 09:01:01 -0700 (PDT) From: CASP5 To: karplus@soe.ucsc.edu Subject: CASP5 targets X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear CASP5 predictor: As you know, the CASP5 prediction experiment has begun. Currently, we are releasing targets at the rate of about one each week day, so as not to over-load the CAFASP servers and processing machinery. We hope to ramp that up to two some days if all continues to run smoothly. But - we will run at of targets before the end of next week. As usual, getting an adequate supply of targets is very hard, so we are asking for your help. One mechanism that worked in CASP4: each prediction group beats the experimental bushes to find at least one target. Personal approaches work MUCH better than mass emailings. What we are asking is that you each approach at least one, more if possible, experimentalists, and make a direct, strong, personal plea that they provide a target, explaining why it is important. Information about the terms of target submission and release, and the submission form are at: http://predictioncenter.llnl.gov/casp5/targets/forms/casp5-tar.html We need all sorts of prediction targets. At this point, it looks as though we may be particularly short of comparative modeling targets. Please get in touch if you have any questions or concerns. Hoping for lots of targets.... John Moult For CASP5 organizers. From karplus@bray.cse.ucsc.edu Mon Jun 17 09:28:41 2002 Date: Mon, 17 Jun 2002 09:28:38 -0700 From: Kevin Karplus To: rost@columbia.edu CC: adamz@llnl.gov, karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu Subject: All 2ry predictions for SAM-T02 server rejected All the secondary structure predictions from the SAM-T02 server were rejected by the CASP5 server, because they used a larger alphabet than EHL. I was under the (perhaps mistaken) impression that CAFASP this year was going to look not only at EHL but also larger alphabets (like EHTL), so our server was set up to predict the full DSSP or STRIDE alphabet. With a little bit of script writing, we can change our server so that the CASP-formatted secondary structure output is collapsed down to a three-letter alphabet (we just need to add up the probabilities for the different codes that collapse to the same letter and choose the largest to report), but then the data for evaluating other alphabets will be lost. Questions: 1) Should we write the script and produce the 3-letter alphabet outputs? Or is CASP/CAFASP interested in having the more detailed predictions? I don't believe we were the only predictors with a larger alphabet on the CAFASP metaserver. 2) What should we do about the 8 targets that have already been processed? I'm not sure if we still have the RDB files with the predictions for the earliest targets, and if we re-run the server, we may get slightly different answers, due to changes in the NR protein sequence database since the first run (We also changed the neural net that the server uses, so a re-run may be quite different.). The codes that we submitted could be converted to the EHL alphabet without summing over all the probabilities that needed to be collapsed together. This is what we had assumed CAFASP would do in the evaluation. We're willing to accept the slight loss of quality that this entails, since the main loss will be in the confidence measure. Thanks for a quick response, Kevin Karplus From rost@columbia.edu Mon Jun 17 17:13:12 2002 MIME-Version: 1.0 Date: Mon, 17 Jun 2002 20:13:09 -0400 From: Burkhard Rost Reply-To: rost@columbia.edu Organization: Columbia University X-Accept-Language: en To: Kevin Karplus CC: adamz@llnl.gov, rachelk@soe.ucsc.edu Subject: Re: All 2ry predictions for SAM-T02 server rejected Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Dear Kevin: how many sec str states do you suggest? as far as I am concerned: - add a state T: ok - add a probability per state: ok however, this means again: change the rules while we go. nowhere explained, is it? b Kevin Karplus wrote: > > All the secondary structure predictions from the SAM-T02 server were > rejected by the CASP5 server, because they used a larger alphabet than EHL. > > I was under the (perhaps mistaken) impression that CAFASP this year > was going to look not only at EHL but also larger alphabets (like > EHTL), so our server was set up to predict the full DSSP or STRIDE alphabet. > > With a little bit of script writing, we can change our server so that > the CASP-formatted secondary structure output is collapsed down to a > three-letter alphabet (we just need to add up the probabilities for > the different codes that collapse to the same letter and choose the > largest to report), but then the data for evaluating other alphabets > will be lost. > > Questions: > 1) Should we write the script and produce the 3-letter > alphabet outputs? Or is CASP/CAFASP interested in having > the more detailed predictions? I don't believe we were the > only predictors with a larger alphabet on the CAFASP metaserver. > > 2) What should we do about the 8 targets that have already > been processed? I'm not sure if we still have the RDB > files with the predictions for the earliest targets, and if > we re-run the server, we may get slightly different > answers, due to changes in the NR protein sequence database > since the first run (We also changed the neural net that the > server uses, so a re-run may be quite different.). > > The codes that we submitted could be converted to the EHL > alphabet without summing over all the probabilities that > needed to be collapsed together. This is what we had > assumed CAFASP would do in the evaluation. We're willing > to accept the slight loss of quality that this entails, > since the main loss will be in the confidence measure. > > Thanks for a quick response, > > Kevin Karplus -- -------------------------------------------------------------- Burkhard Rost CUBIC, Columbia University tel +1-212-305 3773 Dept Biochemistry & Mol Biophysics fax +1-212-305 7932 630 West, 168 Street, BB 217 New York, N.Y. 10032 Mail: rost@columbia.edu WWW: http://www.columbia.edu/~rost/ http://cubic.bioc.columbia.edu/ http://www.c2b2.columbia.edu/ From karplus@bray.cse.ucsc.edu Mon Jun 17 17:36:55 2002 Date: Mon, 17 Jun 2002 17:36:52 -0700 From: Kevin Karplus To: rost@columbia.edu CC: adamz@llnl.gov, rachelk@soe.ucsc.edu, karplus@soe.ucsc.edu In-reply-to: <3D0E7B16.4158EAE9@columbia.edu> (message from Burkhard Rost on Mon, 17 Jun 2002 20:13:09 -0400) Subject: Re: All 2ry predictions for SAM-T02 server rejected I agree that changing the rules as we go is generally a bad idea. But it seems that no attention is paid to the rules or the submission formats between CASP seasons, and attempts to make changes are generally ignored. I had expected that there would be some discussion of CASP prediction formats and such before CASP5, but if there was, I either wasn't on the mailing list or otherwise missed it. I was under the impression that the extra state had already been decided on, but I guess I was confused. I've been pushing (weakly) for the past 4 years to have evaluation of probability vectors, rather than correct/incorrect evaluation, but there has been no attempt to circulate a new format for people to submit the more detailed information. Kevin From rost@columbia.edu Mon Jun 17 17:46:57 2002 MIME-Version: 1.0 Date: Mon, 17 Jun 2002 20:46:54 -0400 From: Burkhard Rost Reply-To: rost@columbia.edu Organization: Columbia University X-Accept-Language: en To: Kevin Karplus CC: adamz@llnl.gov, rachelk@soe.ucsc.edu Subject: Re: All 2ry predictions for SAM-T02 server rejected Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK dear kevin: > I agree that changing the rules as we go is generally a bad idea. glad, you agree > I had expected that there would be some discussion of CASP prediction > formats and such before CASP5, but if there was, I either wasn't on > the mailing list or otherwise missed it. well, sorry, no there wasn't; suppose is my fault. > I was under the impression that the extra state had already been > decided on, but I guess I was confused. I am not aware of that; > I've been pushing (weakly) for the past 4 years to have evaluation of > probability vectors, rather than correct/incorrect evaluation, but > there has been no attempt to circulate a new format for people to > submit the more detailed information. unclear what you mean: 1. matthews is opposed to Q3/SOV: do not believe makes sense at all convince me that i am wrong 2. more than one state: yes, remember that was an issue at the last casp never heard about it after that. what do you suggest? btw: you never responded to my first question: how many states? b > > Kevin -- -------------------------------------------------------------- Burkhard Rost CUBIC, Columbia University tel +1-212-305 3773 Dept Biochemistry & Mol Biophysics fax +1-212-305 7932 630 West, 168 Street, BB 217 New York, N.Y. 10032 Mail: rost@columbia.edu WWW: http://www.columbia.edu/~rost/ http://cubic.bioc.columbia.edu/ http://www.c2b2.columbia.edu/ From karplus@bray.cse.ucsc.edu Mon Jun 17 18:09:26 2002 Date: Mon, 17 Jun 2002 18:09:24 -0700 From: Kevin Karplus To: rost@columbia.edu CC: adamz@llnl.gov, rachelk@soe.ucsc.edu, karplus@soe.ucsc.edu In-reply-to: <3D0E8300.F1691617@columbia.edu> (message from Burkhard Rost on Mon, 17 Jun 2002 20:46:54 -0400) Subject: Re: All 2ry predictions for SAM-T02 server rejected What I have been asking for for evaluation of 2ry-structure prediction is an "information gain" measure. That is sum_positions log (P_est(correct code for position)/P_background(correct code for position)) / number of positions To do this computation, one needs a probability vector output from each predictor, and a background probability vector. The information gain measure is not particularly senstive to how many values there are in the structure alphabet. One can fairly compare an EHL prediction with an EHTL or EBGHISTL prediction. Rachel Karchin (the grad student who put together the SAM-T02 web server) has been investigating many possible local structure alphabets, and the information gain from prediction does seem to be a very useful measure. Because the information gain measure is not very sensitive to alphabet size, my reaction has been to attempt to predict the full range of possible values for an alphabet: EBGHTL for stride, EBGHSTL for DSSP (I dropped the "I" from both because it is so rare---including it would make no discernable difference). The Q6 or Q7 values are naturally much lower that the Q3 values for EHL, and the SOV values drop considerably also (though the SOV(H) and SOV(E) values go up, since we have only real strands and helices in those classes now). The information gained from predicting EBGHTL rather than EHL is moderate---about 0.1 more bits/position if I remember right. Some of the other alphabets that Rachel has been working on provide even more predictable information per position. I think it is too late now that CASP has started to demand a new format from people (though not too late for EVA to start accepting a new format). In any case, I don't have a strong vote for a particular alphabet right now---it would be nice, though, to have CASP accept any subset of DSSP or STRIDE alphabets and collapse them to EHL or EHTL for the evaluation. That is certainly better than rejecting submissions that have done a finer classification. (I recognize that having the servers do the collapse themselves allows them to do more clever collpasing, but I don't really care.) Kevin From jmoult@tunc.org Thu Jun 20 11:15:12 2002 MIME-Version: 1.0 X-Sender: jmoult@indigo5.carb.nist.gov Date: Thu, 20 Jun 2002 14:14:40 -0400 To: bryant@ncbi.nlm.nih.gov, david@mbi.ucla.edu, dfischer@cs.bgu.ac.il, adam@burnham-inst.org, karplus@cse.ucsc.edu, michael.levitt@stanford.edu, lupas@vms.biochem.mpg.de, agm@mrc-lmb.cam.ac.uk, sippl@irina.came.sbg.ac.at, Andrew.Torda@anu.edu.au, shosh@ucmb.ulb.ac.be, yanga@cumbih.bioc.columbia.edu From: John Moult Subject: CASP5 Fold Recognition Consultancy Group Cc: th@sanger.ac.uk, fidelis@llnl.gov, adamz@llnl.gov Content-Type: text/plain; charset="us-ascii"; format=flowed X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK As you know, CASP5 is well underway. In CASPs 3 and 4, consultancy groups were established in comparative modeling, fold recognition and new fold prediction. Members of the groups are veteran CASP predictors, or assessors in previous CASPs. The groups were quite effective at identifying assessors, as well as providing general guidance to the organizers, so we are using the same system again. We are starting a little later this time, so that the basic framework of the experiment is already in place. However, there is still plenty of input needed. We would like you to be a member of the fold recognition group. If you agree to participate, the most pressing first task is the identification of an assessor for the fold recognition category. Note that this time, for each target, three predictors will be asked to assist the assessor, so hopefully the job will not be quite as lonely as in the past. Also, with things running reasonably smoothly at Livermore, assessors should be able to make use of timely evaluation data, reducing the work load. Still, it is still a demanding and key job. Please send your suggestions of suitable people to this email list. I will be the co-ordinator for this consultancy group. John Moult. For CASP5 Organizers. From dfischer@cs.bgu.ac.il Thu Jun 20 15:41:01 2002 MIME-Version: 1.0 X-Authentication-Warning: lace.cs.bgu.ac.il: dfischer owned process doing -bs Date: Fri, 21 Jun 2002 01:35:16 +0300 (IDT) From: Daniel Fischer X-Sender: dfischer@lace To: John Moult cc: bryant@ncbi.nlm.nih.gov, david@mbi.ucla.edu, adam@burnham-inst.org, karplus@cse.ucsc.edu, michael.levitt@stanford.edu, lupas@vms.biochem.mpg.de, agm@mrc-lmb.cam.ac.uk, sippl@irina.came.sbg.ac.at, Andrew.Torda@anu.edu.au, shosh@ucmb.ulb.ac.be, yanga@cumbih.bioc.columbia.edu, th@sanger.ac.uk, fidelis@llnl.gov, adamz@llnl.gov Subject: Re: CASP5 Fold Recognition Consultancy Group In-Reply-To: <5.1.0.14.2.20020620140446.043fc008@indigo5.carb.nist.gov> Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Hi, Why not simply use Livermore's evaluation data as the automatic assessor, without "appointing" a human assessor? Evaluation methods have improved and have become quite sophisticated, and can be used, in my opinion, to rank and grade the groups automatically, with little significant differences from any expert-human assessment. I guess that most predictors I know from CAFASP/LiveBench will be as happy (or more) with a direct, repoducible and automatic evaluation, than with that of a human assessor. Obviously, a human is needed to "interpret" the data (but not too much...), and to prepare and present the tables of ranks, etc. Thus, I think the ideal persons would be the ones who best know the evaluation programs, i.e. the people who wrote them. Dani ------------------ Dr. Daniel Fischer Bioinformatics Dept. of Computer Science Ben Gurion University, Beer-Sheva 84015, Israel Tel +972-8-6472714 e-mail: dfischer@cs.bgu.ac.il Fax +972-8-6477650 or 6477648 http://www.cs.bgu.ac.il/~dfischer On Thu, 20 Jun 2002, John Moult wrote: > As you know, CASP5 is well underway. In CASPs 3 and 4, consultancy groups > were established in comparative modeling, fold recognition and new fold > prediction. Members of the groups are veteran CASP predictors, or assessors > in previous CASPs. The groups were quite effective at identifying > assessors, as well as providing general guidance to the organizers, so we > are using the same system again. We are starting a little later this time, > so that the basic framework of the experiment is already in place. However, > there is still plenty of input needed. We would like you to be a member > of the fold recognition group. > > If you agree to participate, the most pressing first task is the > identification of an assessor for the fold recognition category. Note that > this time, for each target, three predictors will be asked to assist the > assessor, so hopefully the job will not be quite as lonely as in the past. > Also, with things running reasonably smoothly at Livermore, assessors > should be able to make use of timely evaluation data, reducing the work > load. Still, it is still a demanding and key job. Please send your > suggestions of suitable people to this email list. I will be the > co-ordinator for this consultancy group. > > John Moult. > For CASP5 Organizers. > > > From agm@mrc-lmb.cam.ac.uk Fri Jun 21 07:47:44 2002 MIME-Version: 1.0 From: agm@mrc-lmb.cam.ac.uk Subject: Re: CASP5 Fold Recognition Consultancy Group In-Reply-To: <5.1.0.14.2.20020620140446.043fc008@indigo5.carb.nist.gov> from John Moult at "Jun 20, 2002 02:14:40 pm" To: John Moult Date: Fri, 21 Jun 2002 15:47:03 +0100 (BST) CC: bryant@ncbi.nlm.nih.gov, david@mbi.ucla.edu, dfischer@cs.bgu.ac.il, adam@burnham-inst.org, karplus@cse.ucsc.edu, michael.levitt@stanford.edu, lupas@vms.biochem.mpg.de, agm@mrc-lmb.cam.ac.uk, sippl@irina.came.sbg.ac.at, Andrew.Torda@anu.edu.au, shosh@ucmb.ulb.ac.be, yanga@cumbih.bioc.columbia.edu, th@sanger.ac.uk, fidelis@llnl.gov, adamz@llnl.gov Content-Type: text/plain; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Hi, Unlike Dani, I think that there will remain the need in a human assessor unless the accuracy and quality of CASP5 prediction dramatically improved compared to those in CASP3 and 4. I would suggest David Jones or some of the members of former SB-fold team (Rob Russell, Andei Lupas) to volunteer for the job. I like the idea of predictors being involved in the assessment and will be happy to assist the appointed assessor. Apart of reducing the assessor's burden, this will allow the predictors to have learnt for themselves about the difficulty and non-triviality of the assessment. Ialso would propose to increase the number of assistant assessors for each target to 5-7 people who should rate the predictions independently and provide their ratings to the principal assessor. Best regards, Alexey Murzin > As you know, CASP5 is well underway. In CASPs 3 and 4, consultancy groups >were established in comparative modeling, fold recognition and new fold >prediction. Members of the groups are veteran CASP predictors, or assessors >in previous CASPs. The groups were quite effective at identifying >assessors, as well as providing general guidance to the organizers, so we >are using the same system again. We are starting a little later this time, >so that the basic framework of the experiment is already in place. However, >there is still plenty of input needed. We would like you to be a member >of the fold recognition group. > >If you agree to participate, the most pressing first task is the >identification of an assessor for the fold recognition category. Note that >this time, for each target, three predictors will be asked to assist the >assessor, so hopefully the job will not be quite as lonely as in the past. >Also, with things running reasonably smoothly at Livermore, assessors >should be able to make use of timely evaluation data, reducing the work >load. Still, it is still a demanding and key job. Please send your >suggestions of suitable people to this email list. I will be the >co-ordinator for this consultancy group. > >John Moult. >For CASP5 Organizers. > > > > From karplus@bray.cse.ucsc.edu Fri Jun 21 09:56:52 2002 Date: Fri, 21 Jun 2002 09:56:43 -0700 From: Kevin Karplus To: agm@mrc-lmb.cam.ac.uk CC: jmoult@tunc.org, bryant@ncbi.nlm.nih.gov, david@mbi.ucla.edu, dfischer@cs.bgu.ac.il, adam@burnham-inst.org, michael.levitt@stanford.edu, lupas@vms.biochem.mpg.de, agm@mrc-lmb.cam.ac.uk, sippl@irina.came.sbg.ac.at, Andrew.Torda@anu.edu.au, shosh@ucmb.ulb.ac.be, yanga@cumbih.bioc.columbia.edu, th@sanger.ac.uk, fidelis@llnl.gov, adamz@llnl.gov, karplus@soe.ucsc.edu In-reply-to: <200206211447.PAA448440@alf1.mrc-lmb.cam.ac.uk> (agm@mrc-lmb.cam.ac.uk) Subject: Re: CASP5 Fold Recognition Consultancy Group I agree with Alexey---there remains value in having a human assessor look at the predictions. I think, though, that the task may be too big this year---the number of groups participating just in CAFASP is huge, and I suspect that the CASP load will be overwhelming. I certainly don't have the time to be an assessor, and even looking at all the predictions for a couple of targets would probably overwhelm me (since they would be coming in during the school term, when I have a full teaching load). I don't know how we will address the problem of competent assessment---we may have to fall back on Dani's idea of automated assessment, not because automatic assessment is good, but because it is all we can afford. Kevin Karplus From adamz@llnl.gov Mon Jun 24 09:32:20 2002 MIME-Version: 1.0 Sender: adamz@bialko.llnl.gov Date: Mon, 24 Jun 2002 09:32:14 -0700 From: Adam ZEMLA Organization: Lawrence Livermore National Laboratory X-Accept-Language: en To: Kevin Karplus CC: casp5@predictioncenter.llnl.gov Subject: Re: target web page wrong for t0141 Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK It is fixed already, Thank you, Adam Kevin Karplus wrote: > > The web page > > http://predictioncenter.llnl.gov/casp5/targets/cgi/casp5-view.cgi?loc=predictioncenter.llnl.gov;page=casp5/ > > has formatting and link problems for target T0141. > Could you fix them today? > > Thanks, > Kevin Karplus -- *********************************************************************** Adam Zemla, Ph.D. | E-mail: adamz@llnl.gov Biology and Biotechnology Research Program | Phone: (925) 423-5571 Lawrence Livermore National Laboratory, L-448 | Fax: (925) 422-2133 7000 East Ave., Livermore, CA 94550, USA | Bldg: 3751, Room: 109 *********************************************************************** From casp5@bialko.llnl.gov Mon Jun 24 10:43:01 2002 Date: Mon, 24 Jun 2002 10:42:54 -0700 (PDT) From: CASP5 To: karplus@soe.ucsc.edu Subject: CASP5 Prediction Targets X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear CASP5 Predictor, This message is to inform you that 13 targets: T0129 - T0141 are already included in the CASP5 target database at http://PredictionCenter.llnl.gov/casp5/Casp5.html Please check "target list". CASP5 organizers From adamz@llnl.gov Mon Jun 24 17:34:26 2002 MIME-Version: 1.0 Sender: adamz@bialko.llnl.gov Date: Mon, 24 Jun 2002 17:34:19 -0700 From: Adam ZEMLA Organization: Lawrence Livermore National Laboratory X-Accept-Language: en To: rost@columbia.edu CC: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu, adamz@llnl.gov Subject: Re: All 2ry predictions for SAM-T02 server rejected Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Hi Burkhard, There are only two servers (both from Kevin): SAM-T02-server-dssp SAM-T02-server-stride which are submitting models using more than 3 letters code for SS predictions. So, I don't see the larger alphabet output as a common request. If we extend our system to accept other letters (e.g. converting them automatically to H, E, or C) so what we have to do with the confidence level (third column in SS format)? In general, our policy in collecting models for CASP experiment is NOT to introduce any changes into submitted predictions. So, maybe you (CAFASP site) o Kevin (predictor site) can introduce all required changes that comply with CASP format and resubmit models. It is pity that we haven't discuss this issue earlier (before we started CASP5). Adam -------- Original Message -------- Subject: Re: All 2ry predictions for SAM-T02 server rejected Date: Tue, 18 Jun 2002 14:46:14 -0400 From: Burkhard Rost Reply-To: rost@columbia.edu Organization: Columbia University To: Kevin Karplus , adamz@llnl.gov CC: rachelk@soe.ucsc.edu References: <200206171628.g5HGSc322467@bray.cse.ucsc.edu> <3D0E7B16.4158EAE9@columbia.edu> <200206180036.g5I0aqh27700@bray.cse.ucsc.edu> <3D0E8300.F1691617@columbia.edu> <200206180109.g5I19OC26349@bray.cse.ucsc.edu> Dear Kevin: 1. allow CASP/EVA to read just any number of states used by DSSP/STRIDE strongly feel this is what we should do! Dear Adam: a) could you extend the program to cope with other letters? b) are you people able to read more modern files these days? i.e. something like residue 5/Alanine/predicted in state T/with reliability 0.5/with 4 state prediction probability: 0.1 0.2 0.3 0.5 without having to fix the number of states other than somewhere in the header #states HETL ? 2. now about the evaluation, still not clear how to measure success. suggest you convince me that whatever method you propose makes sense. The only way you can do that: show that your score increases the distance between protein pairs of similar structure (start from pdb-select in eva against pdb) closer to one another than non-similar structure... cheers, b Kevin Karplus wrote: > > What I have been asking for for evaluation of 2ry-structure prediction > is an "information gain" measure. That is > > sum_positions log (P_est(correct code for position)/P_background(correct code for position)) > / number of positions > > To do this computation, one needs a probability vector output from > each predictor, and a background probability vector. > > The information gain measure is not particularly senstive to how many > values there are in the structure alphabet. One can fairly compare > an EHL prediction with an EHTL or EBGHISTL prediction. > > Rachel Karchin (the grad student who put together the SAM-T02 web > server) has been investigating many possible local structure > alphabets, and the information gain from prediction does seem to be > a very useful measure. > > Because the information gain measure is not very sensitive to alphabet > size, my reaction has been to attempt to predict the full range of > possible values for an alphabet: EBGHTL for stride, EBGHSTL for DSSP > (I dropped the "I" from both because it is so rare---including it > would make no discernable difference). The Q6 or Q7 values are > naturally much lower that the Q3 values for EHL, and the SOV values > drop considerably also (though the SOV(H) and SOV(E) values go up, > since we have only real strands and helices in those classes now). > The information gained from predicting EBGHTL rather than EHL is > moderate---about 0.1 more bits/position if I remember right. > Some of the other alphabets that Rachel has been working on provide > even more predictable information per position. > > I think it is too late now that CASP has started to demand a new > format from people (though not too late for EVA to start accepting a > new format). > > In any case, I don't have a strong vote for a particular alphabet > right now---it would be nice, though, to have CASP accept any subset > of DSSP or STRIDE alphabets and collapse them to EHL or EHTL for the > evaluation. That is certainly better than rejecting submissions that > have done a finer classification. (I recognize that having the > servers do the collapse themselves allows them to do more clever > collpasing, but I don't really care.) > > Kevin -- -------------------------------------------------------------- Burkhard Rost CUBIC, Columbia University tel +1-212-305 3773 Dept Biochemistry & Mol Biophysics fax +1-212-305 7932 630 West, 168 Street, BB 217 New York, N.Y. 10032 Mail: rost@columbia.edu WWW: http://www.columbia.edu/~rost/ http://cubic.bioc.columbia.edu/ http://www.c2b2.columbia.edu/ From karplus@bray.cse.ucsc.edu Mon Jun 24 20:01:44 2002 Date: Mon, 24 Jun 2002 20:01:42 -0700 From: Kevin Karplus To: adamz@llnl.gov CC: rost@columbia.edu, rachelk@soe.ucsc.edu, karplus@soe.ucsc.edu, learith@soe.ucsc.edu, jcasper@soe.ucsc.edu In-reply-to: <3D17BA8B.39E87AD1@llnl.gov> (message from Adam ZEMLA on Mon, 24 Jun 2002 17:34:19 -0700) Subject: Re: All 2ry predictions for SAM-T02 server rejected We can put together yet another output just for CASP, in which the richer alphabets are collapsed down to 3 states. It make take us a couple of days to get the script tested and installed. I don't know what you want us to do about the targets that have already been submitted---the CAFASP submission is out of our hands. Rachel, the "right" way to do the collapse down to three states would be to take the conditional probability tables P(E| x), P(H|x), P(L|x) for each letter X of each alphabet. Get the (E,H,L) vector for a given network as the product of the conditional probability table with the predicted probabilities: Pnat(E) = sum_x P(E|x) Phat(x). We can then average over the outputs of all the networks to get a 3-state CASP prediction. For the alphabets trained on DSSP or STR, the conditional probabilities are 1 or 0, so the matrix multiply can be simplified. For the ALPHA and STRIDE alphabets, you can get the conditional probability table from the joint probability table computed by compare-real. We can change the web site to provide the RDB, seq, and sequence logo formats for the full alphabets, and provide CASP format for the reduced alphabet. If we do it by averaging over the 4 neural nets trained on different alphabets, we should probably give it a different name---maybe SAM-T02-EHL---to distinguish it from the other predictors. Rachel, if you want to hand this task over to Jenny or Jonathan, I think it would be fine to do so. From adamz@llnl.gov Tue Jun 25 08:50:52 2002 MIME-Version: 1.0 Sender: adamz@bialko.llnl.gov Date: Tue, 25 Jun 2002 08:50:41 -0700 From: Adam ZEMLA Organization: Lawrence Livermore National Laboratory X-Accept-Language: en To: Kevin Karplus CC: rost@columbia.edu, rachelk@soe.ucsc.edu, learith@soe.ucsc.edu, jcasper@soe.ucsc.edu, jmoult@tunc.org Subject: Re: All 2ry predictions for SAM-T02 server rejected Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Dear Kevin, Thank you very much for your decision. Kevin Karplus wrote: > > We can put together yet another output just for CASP, in which the > richer alphabets are collapsed down to 3 states. It make take us a > couple of days to get the script tested and installed. I don't know > what you want us to do about the targets that have already been > submitted---the CAFASP submission is out of our hands. Here is a list of all rejected submissions: PIN_number Registration_code DATE PIN_186784_10747 2491-6940-1261 06/15/02 06:07:31 PIN_188085_10748 5144-8387-2760 06/15/02 06:07:44 PIN_126525_10758 2491-6940-1261 06/15/02 15:01:35 PIN_127826_10759 5144-8387-2760 06/15/02 15:01:48 PIN_156096_10769 2491-6940-1261 06/15/02 15:04:32 PIN_157397_10770 5144-8387-2760 06/15/02 15:04:45 PIN_184548_10781 2491-6940-1261 06/15/02 15:07:11 PIN_185849_10782 5144-8387-2760 06/15/02 15:07:24 PIN_210339_10792 2491-6940-1261 06/15/02 15:09:53 PIN_215640_10793 5144-8387-2760 06/15/02 15:10:06 PIN_236339_10803 2491-6940-1261 06/15/02 15:12:19 PIN_237640_10804 5144-8387-2760 06/15/02 15:12:32 PIN_254915_10808 2491-6940-1261 06/15/02 15:14:19 PIN_274924_10817 5144-8387-2760 06/15/02 15:16:19 PIN_297683_10825 2491-6940-1261 06/15/02 15:18:05 PIN_298984_10826 5144-8387-2760 06/15/02 15:18:18 PIN_226400_10850 2491-6940-1261 06/24/02 08:11:31 PIN_227801_10851 5144-8387-2760 06/24/02 08:11:45 PIN_258531_10862 2491-6940-1261 06/24/02 08:14:52 PIN_263832_10863 5144-8387-2760 06/24/02 08:15:05 PIN_286323_10874 2491-6940-1261 06/24/02 08:17:35 PIN_287624_10875 5144-8387-2760 06/24/02 08:17:48 PIN_314936_10885 2491-6940-1261 06/24/02 08:20:19 PIN_316237_10886 5144-8387-2760 06/24/02 08:20:32 There is a procedure how you can correct your models. For example to correct the model: PIN_186784_10747 1) go to the website: http://PredictionCenter.llnl.gov/casp5/Casp5.html 2) click "Prediction submission facility" 3) enter your email address in the "Email" box 4) paste or type (in the box 3) the PIN_number: PIN_186784_10747 and click "START" 5) following the AUTHOR record add the record: REMARK Corrected submission: PIN_186784_10747 6) introduce all necessary corrections into the model, and click "START" Please follow this procedure with all the models (PIN_numbers) from the list above. Please let me know if you have any questions, Adam > > Rachel, the "right" way to do the collapse down to three states would > be to take the conditional probability tables P(E| x), P(H|x), P(L|x) > for each letter X of each alphabet. Get the (E,H,L) vector for a > given network as the product of the conditional probability table with > the predicted probabilities: Pnat(E) = sum_x P(E|x) Phat(x). We can > then average over the outputs of all the networks to get a 3-state > CASP prediction. > > For the alphabets trained on DSSP or STR, the conditional > probabilities are 1 or 0, so the matrix multiply can be simplified. > For the ALPHA and STRIDE alphabets, you can get the conditional > probability table from the joint probability table computed by > compare-real. > > We can change the web site to provide the RDB, seq, and sequence logo > formats for the full alphabets, and provide CASP format for the > reduced alphabet. If we do it by averaging over the 4 neural nets > trained on different alphabets, we should probably give it a different > name---maybe SAM-T02-EHL---to distinguish it from the other predictors. > > Rachel, if you want to hand this task over to Jenny or Jonathan, I > think it would be fine to do so. -- *********************************************************************** Adam Zemla, Ph.D. | E-mail: adamz@llnl.gov Biology and Biotechnology Research Program | Phone: (925) 423-5571 Lawrence Livermore National Laboratory, L-448 | Fax: (925) 422-2133 7000 East Ave., Livermore, CA 94550, USA | Bldg: 3751, Room: 109 *********************************************************************** From rachelk@grunt.cse.ucsc.edu Mon Jul 1 10:45:40 2002 MIME-Version: 1.0 From: Rachel Karchin Content-Type: text/plain; charset=us-ascii Date: Mon, 1 Jul 2002 10:45:32 -0700 To: "Leszek Rychlewski" CC: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu Subject: SAM_T02 scores now good X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Hi Leszek: We've worked on improving the quality of the E-value scores that SAM_T02 reports for each predicted (.al) model, and think they are now meaningful enough to be useful. Please go ahead and include SAM_T02's .al E-values along with FSSP rep and SCOP domain on the CAFASP summary pages for each target. Thanks! -- rk ------------------------------------------------------------------------- Rachel Karchin bioinformatics Ph.D. candidate Office phone: (831) 459-5431 http://www.cse.ucsc.edu/~rachelk email: rachelk@cse.ucsc.edu From leszek@bioinfo.pl Mon Jul 1 10:54:02 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Rachel Karchin" Cc: Subject: RE: SAM_T02 scores now good Date: Mon, 1 Jul 2002 19:54:23 +0200 Content-Type: text/plain; charset="Windows-1252" X-Priority: 3 (Normal) X-MSMail-Priority: Normal In-Reply-To: <15648.38204.692038.571816@grunt.cse.ucsc.edu> Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Dear Rachel, The scores will be automatically included in You provide the "REMARK SCORE ..." or "SCORE ..." record in the AL formatted result mails. Still it will be impossible to compare the specificity of the scores with other servers if You don't provide the scores for the previous models. Nevertheless the new info will help the users. Best regards, Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl > -----Original Message----- > From: Rachel Karchin [mailto:rachelk@soe.ucsc.edu] > Sent: Monday, July 01, 2002 7:46 PM > To: Leszek Rychlewski > Cc: karplus@soe.ucsc.edu; rachelk@soe.ucsc.edu > Subject: SAM_T02 scores now good > > > Hi Leszek: > > We've worked on improving the quality of the E-value scores > that SAM_T02 reports for each predicted (.al) model, and think > they are now meaningful enough to be useful. > > Please go ahead and include SAM_T02's .al E-values along with > FSSP rep and SCOP domain on the CAFASP summary pages for each > target. > > Thanks! > > -- rk > > ------------------------------------------------------------------------- > Rachel Karchin > bioinformatics Ph.D. candidate > Office phone: (831) 459-5431 > http://www.cse.ucsc.edu/~rachelk > email: rachelk@cse.ucsc.edu > From rachelk@grunt.cse.ucsc.edu Tue Jul 2 15:02:13 2002 MIME-Version: 1.0 From: Rachel Karchin Content-Type: text/plain; charset=us-ascii Date: Tue, 2 Jul 2002 15:02:08 -0700 To: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu Subject: Re: All 2ry predictions for SAM-T02 server rejected In-Reply-To: <15650.8777.881470.125909@grunt.cse.ucsc.edu> X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Kevin -- here's a copy of message I just sent to CASP/CAFASP: (original cc to you bounced back on me due to typo) Dear Burkhard, Adam and Leszek: We've written the code to produce another secondary structure prediction output just for CASP, which collapses the richer local structure alphabets down to 3 states. Here are some questions: -- for CAFASP, when a request includes CaspResults=on, we currently send out three emails of prediction results with these subject lines: o SAM_T02 CASP models (FR .al files) o sam-t02-stride (stride-EBGHTL prediction) o sam-t02-dssp (dssp-EBGHSTL prediction) I would like to add a fourth email of prediction results: o sam-t02-dssp-ehl This will be the three-state prediction in CASP format. We'd like to continue to submit the full dssp and stride predictions to EVA. Does this work for you? -- for CASP, we are registered as four "groups", three of which are for automated predictions: SAM-T02-server 5035-2079-5263 SAM-T02-server-dssp 2491-6940-1261 SAM-T02-server-stride 5144-8387-2760 but since they will not be evaluated for CASP, should we discontinue SAM-T02-server-dssp and SAM-T02-server-stride? How does one discontinue a CASP group? Also, how do we register our new dssp-ehl group? Should we re-use the SAM-T02-server-dssp membership for the new predictions? -- rk ------------------------------------------------------------------------- Rachel Karchin bioinformatics Ph.D. candidate Office phone: (831) 459-5431 http://www.cse.ucsc.edu/~rachelk email: rachelk@cse.ucsc.edu From jmoult@tunc.org Wed Jul 3 08:17:44 2002 MIME-Version: 1.0 X-Sender: jmoult@indigo5.carb.nist.gov Date: Wed, 03 Jul 2002 11:17:04 -0400 To: Rachel Karchin , rost@columbia.edu, adamz@llnl.gov, leszek@bioinfo.pl, karplus@soe.ucsc.edu, learithe@soe.ucsc.edu, jcasper@soe.ucsc.edu From: John Moult Subject: Re: All 2ry predictions for SAM-T02 server rejected] Content-Type: text/plain; charset="us-ascii"; format=flowed X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Dear Rachel: Adam Zemla forwarded your message to me. We suggest you do the following: 1. Register the new server at CASP. 2. Reformat all the predictions you have already submitted in the non-CASP acceptable mode, and resubmit them to the new server. I understand that reformatting rather than re-running is needed, as the databases you use have changed in the meanwhile? (Adam and Burkhard - please clarify whether these submissions should go directly to Livermore, or via Columbia). 3. From now on, submit all predictions, in CASP format, under the new server ID. Does that make sense? Thanks very much for taking care of this. Unclear to me how we got to this point - I was not aware of a proposed alternative. John Moult. At 04:00 PM 7/2/2002 -0700, you wrote: >-------- Original Message -------- >Subject: Re: All 2ry predictions for SAM-T02 server rejected >Date: Tue, 2 Jul 2002 14:59:37 -0700 >From: Rachel Karchin >To: rost@columbia.edu, adamz@llnl.gov, leszek@bioinfo.pl >CC: karplus@soe.ucsc.edu.rachelk@soe.ucsc.edu, >learithe@soe.ucsc.edu,jcasper@soe.ucsc.edu >References: ><3D17BA8B.39E87AD1@llnl.gov><200206250301.g5P31gH10174@bray.cse.ucsc.edu> > >Dear Burkhard, Adam and Leszek: > >We've written the code to produce another secondary structure >prediction output just for CASP, which collapses the >richer local structure alphabets down to 3 states. > >Here are some questions: > >-- for CAFASP, when a request includes CaspResults=on, we currently > send out three emails of prediction results with these subject lines: > > o SAM_T02 CASP models (FR .al files) > o sam-t02-stride (stride-EBGHTL prediction) > o sam-t02-dssp (dssp-EBGHSTL prediction) > >I would like to add a fourth email of prediction results: > > o sam-t02-dssp-ehl > >This will be the three-state prediction in CASP format. >We'd like to continue to submit the full dssp and stride >predictions to EVA. > >Does this work for you? > >-- for CASP, we are registered as four "groups", three of > which are for automated predictions: > > >SAM-T02-server 5035-2079-5263 >SAM-T02-server-dssp 2491-6940-1261 >SAM-T02-server-stride 5144-8387-2760 > >but since they will not be evaluated for CASP, should we >discontinue SAM-T02-server-dssp and SAM-T02-server-stride? > >How does one discontinue a CASP group? > >Also, how do we register our new dssp-ehl group? Should we re-use >the SAM-T02-server-dssp membership for the new predictions? > >-- rk > >------------------------------------------------------------------------- >Rachel Karchin >bioinformatics Ph.D. candidate >Office phone: (831) 459-5431 >http://www.cse.ucsc.edu/~rachelk >email: rachelk@cse.ucsc.edu From rachelk@grunt.cse.ucsc.edu Wed Jul 3 12:13:42 2002 MIME-Version: 1.0 From: Rachel Karchin Content-Type: text/plain; charset=us-ascii Date: Wed, 3 Jul 2002 12:13:37 -0700 To: "Leszek Rychlewski" , rost@columbia.edu CC: karplus@soe.ucsc.edu Subject: samt99, samt02 down on July 4, 2002 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear Leszek and Burkhard: Our system administrator tells us that all our systems are going down for maintenance on July 4, the American Independence Day. Any targets submitted to the servers on July 4 (California time) probably will not get processed. We've been told that the systems will be back up by July 5, and would appreciate if you could re-submit any targets from July 4 on the 5th. Thanks for your patience. -- rk ------------------------------------------------------------------------- Rachel Karchin bioinformatics Ph.D. candidate Office phone: (831) 459-5431 http://www.cse.ucsc.edu/~rachelk email: rachelk@cse.ucsc.edu From leszek@bioinfo.pl Wed Jul 3 12:29:07 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Rachel Karchin" , Cc: Subject: RE: samt99, samt02 down on July 4, 2002 Date: Wed, 3 Jul 2002 21:29:30 +0200 Content-Type: text/plain; charset="Windows-1252" X-Priority: 3 (Normal) X-MSMail-Priority: Normal In-Reply-To: <15651.19681.210138.244145@grunt.cse.ucsc.edu> Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK no problem, Leszek > -----Original Message----- > From: Rachel Karchin [mailto:rachelk@soe.ucsc.edu] > Sent: Wednesday, July 03, 2002 9:14 PM > To: Leszek Rychlewski; rost@columbia.edu > Cc: karplus@soe.ucsc.edu > Subject: samt99, samt02 down on July 4, 2002 > > > Dear Leszek and Burkhard: > > Our system administrator tells us that all our systems are > going down for maintenance on July 4, the American Independence > Day. > > Any targets submitted to the servers on July 4 (California time) > probably will not get processed. > > We've been told that the systems will be back up by July 5, and > would appreciate if you could re-submit any targets from July 4 > on the 5th. > > Thanks for your patience. > > -- rk > > ------------------------------------------------------------------------- > Rachel Karchin > bioinformatics Ph.D. candidate > Office phone: (831) 459-5431 > http://www.cse.ucsc.edu/~rachelk > email: rachelk@cse.ucsc.edu > From rachelk@grunt.cse.ucsc.edu Wed Jul 3 18:20:27 2002 Return-Path: Received: from grunt.cse.ucsc.edu (grunt.cse.ucsc.edu [128.114.50.248]) by services.cse.ucsc.edu (8.12.1/8.12.1) with ESMTP id g641KQcD000777; Wed, 3 Jul 2002 18:20:26 -0700 (PDT) Received: (from rachelk@localhost) by grunt.cse.ucsc.edu (8.11.6/8.11.4) id g641KMl24227; Wed, 3 Jul 2002 18:20:22 -0700 From: Rachel Karchin MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="3EupwF+Hcs" Content-Transfer-Encoding: 7bit Message-ID: <15651.41686.432448.904489@grunt.cse.ucsc.edu> Date: Wed, 3 Jul 2002 18:20:22 -0700 To: volker@chem.columbia.edu Cc: rost@columbia.edu, Rachel Karchin , leszek@bioinfo.pl, "Karplus,Kevin" , learithe@soe.ucsc.edu, jcasper@soe.ucsc.edu Subject: SAM-T02 dssp-ehl conversion script In-Reply-To: <3D233D47.17B1E2FC@llnl.gov> References: <3D17BA8B.39E87AD1@llnl.gov> <200206250301.g5P31gH10174@bray.cse.ucsc.edu> <15650.8777.881470.125909@grunt.cse.ucsc.edu> <3D2335F3.9090302@columbia.edu> <3D233D47.17B1E2FC@llnl.gov> X-Mailer: VM 7.00 under Emacs 21.1.1 --3EupwF+Hcs Content-Type: text/plain; charset=us-ascii Content-Description: message body text Content-Transfer-Encoding: 7bit Hi Eyrich: We have put together a pair of scripts that you can use to convert our rejected dssp and stride CASP submissions to an acceptable DSSP three-letter format. The first script is called RDBCombine. It takes as input two rdb files of predictions (one for stride-ebghtl and one for dssp-ebghstl) and merges them into a single rdb file for dssp-ehl. The second script is called rdb2casp, and it converts the output of RDBCombine into CASP format. Attached please find a zipped tarball containing: the two scripts -- rdb2casp -- RDBCombine two perl modules that the scripts depend on -- RDBParse.pm -- ParseCompare.pm a pair of rdb files for each of our rejected targets two files containing alphabet translation information -- t2k.stride-dssp_ehl2.compare -- t2k.dssp-dssp_ehl2.compare Usage: Unpack all files in the tarball into a single directory. step 1: convert a pair (T0XXX.t2k.dssp-ebghstl.rdb, T0XXX.t2k.stride-ebghtl.rdb) to T0XXX.t2k.dssp-ehl.rdb RDBCombine -a AUTHOR T0XXX.t2k.dssp-ebghstl.rdb \ T0XXX.t2k.stride-ebghtl.rdb > T0XXX.t2k.dssp-ehl.rdb You may have to do this twice, since we need resubmissions for both CASP and CAFASP. The AUTHOR for CASP should be: 5661-1766-5511 The AUTHOR for CAFASP should be: 1549-8716-6404 step 2: convert T0XXX.t2k.dssp-ehl.rdb to CASP format rdb2casp T0XXX.t2k.dssp-ehl.rdb > T0XXX.t2k.dssp-ehl If you have problems or questions, please let us know. Yours truly, Rachel and Jonathan rachelk@soe.ucsc.edu jcasper@soe.ucsc.edu Adam ZEMLA writes: > Burkhard Rost wrote: > > > > my suggestion: > > just add group 4 (and give us a script that does the conversion > > of the old predictions) ... > > > > adam: what is yours? > > b > > Yes, it is fine with us. > Rachel: please register your new sam-t02-dssp-ehl server > for CASP and CAFASP, and send a script to Eyrich Volker. --3EupwF+Hcs Content-Type: application/octet-stream Content-Description: SAM T02 DSSP converter kit Content-Disposition: attachment; filename="SAM_T02_DSSP_converter.tar.gz" Content-Transfer-Encoding: base64 H4sICMOeIz0AA1NBTV9UMDJfRFNTUF9jb252ZXJ0ZXIudGFyAOz9XbMt2XEcCPbrOb+izPTSY9ak cn1nPqIFEIABpAEoDGl8pERIwogiNQBosulfPxnhvlZ47sx9UVSrq7qJupIdXtxaJ3fuzPUR4e7h 8ef/9tdbysef/yH/lz//+9///r/92W/+/X/6z7//wz/8+e/+/t//L/+T/mxp23qv/8t2/smj2f/N tWz+v8+/ppHPfxt1lG2rKadzfKtt+1++2v5n3cCX/vzz7//wd7/76qv/5b/83e/+2z/88+/fjvtv 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(dfischer@lace [132.72.40.8]) by indigo.cs.bgu.ac.il (8.11.0/8.11.0) with ESMTP id g650tei20849 for ; Fri, 5 Jul 2002 03:55:41 +0300 (IDT) From: Daniel Fischer Received: (dfischer@localhost) by lace.cs.bgu.ac.il (8.8.8+Sun/8.6.9) id DAA15797 for karplus@cse.ucsc.edu; Fri, 5 Jul 2002 03:56:31 +0300 (IDT) Date: Fri, 5 Jul 2002 03:56:31 +0300 (IDT) Message-Id: <200207050056.DAA15797@lace.cs.bgu.ac.il> To: karplus@cse.ucsc.edu X-SpamBouncer: 1.4 (10/07/01) X-SBRule: Pattern Match (Disclaimer) (Score: 1100) X-SBPass: No Freemail Filtering X-SBClass: Blocked Dear CAFASP participant, As a CAFASP participant, we would like to invite you to participate in an additional experiment called PDB-CAFASP. The goal of PDB-CAFASP, like CAFASP, is to evaluate the performance of 3D structure prediction servers, but using a larger number of targets. The larger the set of targets, the more significant the comparative evaluation of the servers' performance will be. The set of targets for PDB-CAFASP will be taken from the "pre-release" PDB entries. Pre-release PDB entries are entries soon to be released, whose structures are not yet published, but whose sequence is known. PDB-CAFASP is planned to take place between the end of July until November. If you would like to have your server included in PDB-CAFASP, please send us a message to register. Servers will be included in PDB-CAFASP only if such a message is received. Further details appear at the CAFASP website at http://www.cs.bgu.ac.il/~dfischer/CAFASP3. We hope to see your server in PDB-CAFASP! (If you want to be removed from the CAFASP mail-list, please reply with an "unsubscribe CAFASP" message). From leszek@bioinfo.pl Wed Jul 10 01:27:31 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Kevin Karplus" , Cc: Subject: RE: Is t99 web site working? Date: Wed, 10 Jul 2002 10:28:02 +0200 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 In-Reply-To: <200207100051.g6A0pY622696@bray.cse.ucsc.edu> Importance: Normal X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK - I have sent the next target T0150 to see if I get a response from SamT99. - I have also sent the T0148 target to samt02, where I did not get a response yet. Yours, Leszek > -----Original Message----- > From: Kevin Karplus [mailto:karplus@soe.ucsc.edu] > Sent: Wednesday, July 10, 2002 2:52 AM > To: stu@soe.ucsc.edu > Cc: karplus@soe.ucsc.edu; leszek@bioinfo.pl; rachelk@soe.ucsc.edu > Subject: Is t99 web site working? > > > > Spencer, > > I noticed that the CAFASP server says "busy" for SAM-T99 for several > of the recent targets. Is the server not responding correctly? > The SAM-T2K server seems to be working fine, so I don't think it is a > global issue with the cluster. > > Spencer, please check that the t99 server is working, then send Leszek > a note, so he can resubmit any sam-t99 targets for which he hasn't > gotten a response. > > Kevin > From rachelk@grunt.cse.ucsc.edu Tue Jul 16 06:41:24 2002 MIME-Version: 1.0 From: Rachel Karchin Content-Type: text/plain; charset=us-ascii Date: Tue, 16 Jul 2002 06:41:21 -0700 To: Volker Eyrich Cc: Rachel Karchin , karplus@soe.ucsc.edu Subject: Re: SAM-T02 dssp-ehl conversion script In-Reply-To: X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Did you have success using the conversion scripts I sent you? Please confirm that the SAM_T02 predictions for the rejected targets were resubmitted and accepted. Thanks. -- rk ------------------------------------------------------------------------- Rachel Karchin bioinformatics Ph.D. candidate Office phone: (831) 459-5431 http://www.cse.ucsc.edu/~rachelk email: rachelk@cse.ucsc.edu From rachelk@grunt.cse.ucsc.edu Tue Jul 16 13:42:22 2002 MIME-Version: 1.0 From: Rachel Karchin Content-Type: text/plain; charset=us-ascii Date: Tue, 16 Jul 2002 13:42:13 -0700 To: rost@columbia.edu Cc: Rachel Karchin , adamz@llnl.gov, leszek@bioinfo.pl, "Karplus,Kevin" , learithe@soe.ucsc.edu, jcasper@soe.ucsc.edu, "Eyrich,Volker" Subject: Re: All 2ry predictions for SAM-T02 server rejected In-Reply-To: <3D2335F3.9090302@columbia.edu> X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Hi Burkhard, Adam and Leszek: Volker has told me that he will be submitting our converted SAM_T02 DSSP-ehl predictions for T0129 through T0145 tonight. The targets later than T0145 (from T0146 on) have had DSSP-ehl predictions automatically generated by the SAM_T02 server. As we discussed, these predictions come in the form of an email titled sam-t02-dssp-ehl. We haven't gotten any confirmations from CASP or CAFASP for the automated dssp-ehl predictions. Have they been received and accepted? Are they being correctly forwarded to Burkhard and Adam? The SAM-T02 dssp-ehl CASP id is: 5661-1766-5511 The SAM-T02 dssp-ehl CAFASP id is: 1549-8716-6404 Yours truly, -- rk ------------------------------------------------------------------------- Rachel Karchin bioinformatics Ph.D. candidate Office phone: (831) 459-5431 http://www.cse.ucsc.edu/~rachelk email: rachelk@cse.ucsc.edu From rachelk@grunt.cse.ucsc.edu Tue Jul 16 16:15:43 2002 MIME-Version: 1.0 From: Rachel Karchin Content-Type: text/plain; charset=us-ascii Date: Tue, 16 Jul 2002 16:15:38 -0700 To: rost@columbia.edu Cc: rachelk@soe.ucsc.edu, karplus@soe.ucsc.edu Subject: Re: [Fwd: Re: [Fwd: Re: All 2ry predictions for SAM-T02 server rejected]] In-Reply-To: <3D34A46A.3060808@columbia.edu> X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Burkhard Rost writes: > rachel: what was your email about then? > b Volker converted T0129 through T0145, but we want to make sure you've gotten all targets subsequent to T0145. We haven't gotten any confirmations about these. -- rk > > -------- Original Message -------- > Subject: Re: [Fwd: Re: All 2ry predictions for SAM-T02 server rejected] > Date: Tue, 16 Jul 2002 18:16:08 -0400 (EDT) > From: Volker Eyrich > To: Burkhard Rost > > > it's all cool ... _I_ converted the existing ones for them ... > > -V > > On Tue, 16 Jul 2002, Burkhard Rost wrote: > > > volker: > > don't get it; > > > > they did not simply 'convert' the old ones, but do them again? > > b > > > > -------- Original Message -------- > > Subject: Re: All 2ry predictions for SAM-T02 server rejected > > Date: Tue, 16 Jul 2002 13:42:13 -0700 > > From: Rachel Karchin > > To: rost@columbia.edu > > CC: Rachel Karchin , adamz@llnl.gov, > > leszek@bioinfo.pl, "Karplus,Kevin" , > > learithe@soe.ucsc.edu, jcasper@soe.ucsc.edu, "Eyrich,Volker" > > > > References: <3D17BA8B.39E87AD1@llnl.gov> <200206250301.g5P31gH10174@bray.cse.ucsc.edu> <15650.8777.881470.125909@grunt.cse.ucsc.edu> <3D2335F3.9090302@columbia.edu> > > > > Hi Burkhard, Adam and Leszek: > > > > Volker has told me that he will be submitting our converted > > SAM_T02 DSSP-ehl predictions for T0129 through T0145 tonight. > > > > The targets later than T0145 (from T0146 on) have had DSSP-ehl > > predictions automatically generated by the SAM_T02 server. > > As we discussed, these predictions come in the form of an email > > titled sam-t02-dssp-ehl. > > > > We haven't gotten any confirmations from CASP or CAFASP for > > the automated dssp-ehl predictions. > > > > Have they been received and accepted? Are they being correctly > > forwarded to Burkhard and Adam? > > > > The SAM-T02 dssp-ehl CASP id is: 5661-1766-5511 > > The SAM-T02 dssp-ehl CAFASP id is: 1549-8716-6404 > > > > Yours truly, > > > > -- rk > > > > ------------------------------------------------------------------------- > > Rachel Karchin > > bioinformatics Ph.D. candidate > > Office phone: (831) 459-5431 > > http://www.cse.ucsc.edu/~rachelk > > email: rachelk@cse.ucsc.edu > > > > > > -- > > -------------------------------------------------------------- > > Burkhard Rost > > CUBIC, Columbia University tel +1-212-305 3773 > > Dept Biochemistry & Mol Biophysics fax +1-212-305 7932 > > 630 West, 168 Street, BB 217 > > New York, N.Y. 10032 > > Mail: rost@columbia.edu > > WWW: http://www.columbia.edu/~rost/ > > http://cubic.bioc.columbia.edu/ > > http://www.c2b2.columbia.edu/ > > > > > > -- > -------------------------------------------------------------- > Burkhard Rost > CUBIC, Columbia University tel +1-212-305 3773 > Dept Biochemistry & Mol Biophysics fax +1-212-305 7932 > 630 West, 168 Street, BB 217 > New York, N.Y. 10032 > Mail: rost@columbia.edu > WWW: http://www.columbia.edu/~rost/ > http://cubic.bioc.columbia.edu/ > http://www.c2b2.columbia.edu/ From rachelk@grunt.cse.ucsc.edu Tue Jul 16 16:45:37 2002 MIME-Version: 1.0 From: Rachel Karchin Content-Type: text/plain; charset=us-ascii Date: Tue, 16 Jul 2002 16:45:34 -0700 To: karplus@soe.ucsc.edu Subject: Re: [Fwd: Re: [Fwd: Re: All 2ry predictions for SAM-T02 server rejected]] In-Reply-To: <3D34AF79.90605@columbia.edu> X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Kevin, here is Burkhard's reply to my inquiry about our submissions. -- rk Burkhard Rost writes: > he got it; i got it ... > b > > Rachel Karchin wrote: > > Burkhard Rost writes: > > > >>rachel: what was your email about then? > >>b > > > > > > Volker converted T0129 through T0145, but we want to make sure > > you've gotten all targets subsequent to T0145. We haven't > > gotten any confirmations about these. > > > > -- rk From adamz@llnl.gov Tue Jul 16 17:08:36 2002 MIME-Version: 1.0 Sender: adamz@bialko.llnl.gov Date: Tue, 16 Jul 2002 17:08:28 -0700 From: Adam ZEMLA Organization: Lawrence Livermore National Laboratory X-Accept-Language: en To: Rachel Karchin CC: rost@columbia.edu, leszek@bioinfo.pl, "Karplus,Kevin" , learithe@soe.ucsc.edu, jcasper@soe.ucsc.edu, "Eyrich,Volker" , adamz@llnl.gov, jmoult@tunc.org Subject: Re: All 2ry predictions for SAM-T02 server rejected Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear Rachel, I am sending you information about all registrations made by your site. 5661-1766-5511 is an account under Kevin Karplus name registered as a regular CASP5 predictor. Below there are server registrations that can be used for CAFASP predictions: 2491-6940-1261 SAM-T02-server-dssp no models (all rejected) 5144-8387-2760 SAM-T02-server-stride no models (all rejected) 1549-8716-6404 SAM-T02-server-dssp-ehl no models have been submitted for this account. Burkhard and Volker, please investigate why this is the case. 6269-7633-6117 SAM-T99 mixture of TS and SS models collected. 5035-2079-5263 SAM-T02-server TS models collected. Rachel Karchin wrote: > > Hi Burkhard, Adam and Leszek: > > Volker has told me that he will be submitting our converted > SAM_T02 DSSP-ehl predictions for T0129 through T0145 tonight. OK, now I can remove the two servers, 2491-6940-1261 and 5144-8387-2760, from CASP5 database. Yes? Regards, Adam > > The targets later than T0145 (from T0146 on) have had DSSP-ehl > predictions automatically generated by the SAM_T02 server. > As we discussed, these predictions come in the form of an email > titled sam-t02-dssp-ehl. > > We haven't gotten any confirmations from CASP or CAFASP for > the automated dssp-ehl predictions. > > Have they been received and accepted? Are they being correctly > forwarded to Burkhard and Adam? > > The SAM-T02 dssp-ehl CASP id is: 5661-1766-5511 > The SAM-T02 dssp-ehl CAFASP id is: 1549-8716-6404 > > Yours truly, > > -- rk > > ------------------------------------------------------------------------- > Rachel Karchin > bioinformatics Ph.D. candidate > Office phone: (831) 459-5431 > http://www.cse.ucsc.edu/~rachelk > email: rachelk@cse.ucsc.edu -- *********************************************************************** Adam Zemla, Ph.D. | E-mail: adamz@llnl.gov Biology and Biotechnology Research Program | Phone: (925) 423-5571 Lawrence Livermore National Laboratory, L-448 | Fax: (925) 422-2133 7000 East Ave., Livermore, CA 94550, USA | Bldg: 3751, Room: 109 *********************************************************************** From karplus@bray.cse.ucsc.edu Tue Jul 16 17:16:08 2002 Date: Tue, 16 Jul 2002 17:16:04 -0700 From: Kevin Karplus To: adamz@llnl.gov CC: rachelk@soe.ucsc.edu, rost@columbia.edu, leszek@bioinfo.pl, learithe@soe.ucsc.edu, jcasper@soe.ucsc.edu, volker@chem.columbia.edu, adamz@llnl.gov, jmoult@tunc.org, karplus@soe.ucsc.edu In-reply-to: <3D34B57C.9DA2030E@llnl.gov> (message from Adam ZEMLA on Tue, 16 Jul 2002 17:08:28 -0700) Subject: Re: All 2ry predictions for SAM-T02 server rejected The servers 2491-6940-1261 and 5144-8387-2760 were not providing CASP-legal secondary structure predictions (too large an alphabet), and so should be removed from the CASP5 database. We provided a script to Rost and Volker to convert the older CAFASP submissions (up through about T0145) to legal CASP format (collapsing the alphabets) to be submitted as DSSP-ehl predictions 1549-8716-6404, and started about then submitting DSSP-ehl predictions directly to CAFASP. The ones we submitted directly will differ somewhat from one produced by the script we sent Volker, as the newer predictions combine three neural-network outputs instead of two (we did not provide the third neural network output to CAFASP for the earlier targets, so thought it inappropriate to go "back in time" on those targets). Kevin Karplus From volker@chem.columbia.edu Tue Jul 16 18:49:06 2002 MIME-Version: 1.0 X-Authentication-Warning: euphrates.chem.columbia.edu: volker owned process doing -bs Date: Tue, 16 Jul 2002 21:49:38 -0400 (EDT) From: Volker Eyrich X-X-Sender: To: Adam ZEMLA cc: Rachel Karchin , , , "Karplus,Kevin" , , , Subject: Re: All 2ry predictions for SAM-T02 server rejected In-Reply-To: <3D34B57C.9DA2030E@llnl.gov> Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Hi all, I just submitted SAM-T02-server-dssp-ehl predictions (predictor code: 1549-8716-6404) for targets T0129 - T0154. Adam, can you please let me know whether they passed the verification process. T0155 and T0156 will follow soon (together with the predictions from all the other servers). bye, Volker PS: FYI ... the delays were basically due to me not being around much last week ... On Tue, 16 Jul 2002, Adam ZEMLA wrote: > Dear Rachel, > > I am sending you information about all registrations made by your site. > > 5661-1766-5511 is an account under Kevin Karplus name registered > as a regular CASP5 predictor. > > Below there are server registrations that can be used for CAFASP > predictions: > > 2491-6940-1261 SAM-T02-server-dssp no models (all rejected) > 5144-8387-2760 SAM-T02-server-stride no models (all rejected) > > 1549-8716-6404 SAM-T02-server-dssp-ehl no models have been submitted > for this account. Burkhard and Volker, please investigate why this is > the case. > > 6269-7633-6117 SAM-T99 mixture of TS and SS models collected. > > 5035-2079-5263 SAM-T02-server TS models collected. > > Rachel Karchin wrote: > > > > Hi Burkhard, Adam and Leszek: > > > > Volker has told me that he will be submitting our converted > > SAM_T02 DSSP-ehl predictions for T0129 through T0145 tonight. > > OK, now I can remove the two servers, 2491-6940-1261 and 5144-8387-2760, > from CASP5 database. Yes? > > Regards, > Adam > > > > > The targets later than T0145 (from T0146 on) have had DSSP-ehl > > predictions automatically generated by the SAM_T02 server. > > As we discussed, these predictions come in the form of an email > > titled sam-t02-dssp-ehl. > > > > We haven't gotten any confirmations from CASP or CAFASP for > > the automated dssp-ehl predictions. > > > > Have they been received and accepted? Are they being correctly > > forwarded to Burkhard and Adam? > > > > The SAM-T02 dssp-ehl CASP id is: 5661-1766-5511 > > The SAM-T02 dssp-ehl CAFASP id is: 1549-8716-6404 > > > > Yours truly, > > > > -- rk > > > > ------------------------------------------------------------------------- > > Rachel Karchin > > bioinformatics Ph.D. candidate > > Office phone: (831) 459-5431 > > http://www.cse.ucsc.edu/~rachelk > > email: rachelk@cse.ucsc.edu > > -- > > *********************************************************************** > Adam Zemla, Ph.D. | E-mail: adamz@llnl.gov > Biology and Biotechnology Research Program | Phone: (925) 423-5571 > Lawrence Livermore National Laboratory, L-448 | Fax: (925) 422-2133 > 7000 East Ave., Livermore, CA 94550, USA | Bldg: 3751, Room: 109 > *********************************************************************** > From adamz@llnl.gov Tue Jul 16 19:15:04 2002 MIME-Version: 1.0 Sender: adamz@bialko.llnl.gov Date: Tue, 16 Jul 2002 19:14:23 -0700 From: Adam ZEMLA Organization: Lawrence Livermore National Laboratory X-Accept-Language: en To: Volker Eyrich CC: Rachel Karchin , rost@columbia.edu, leszek@bioinfo.pl, "Karplus,Kevin" , learithe@soe.ucsc.edu, jcasper@soe.ucsc.edu, jmoult@tunc.org Subject: Re: All 2ry predictions for SAM-T02 server rejected Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Volker Eyrich wrote: > > Hi all, > > I just submitted SAM-T02-server-dssp-ehl predictions (predictor code: > 1549-8716-6404) for targets T0129 - T0154. Adam, can you please let me > know whether they passed the verification process. T0155 and T0156 will > follow soon (together with the predictions from all the other servers). > > bye, > > Volker Volker, thank you very much for your great work. All models passed the verification process. So, now I am removing 2491-6940-1261 and 5144-8387-2760 servers from the CASP5 database. Regards, Adam -- *********************************************************************** Adam Zemla, Ph.D. | E-mail: adamz@llnl.gov Biology and Biotechnology Research Program | Phone: (925) 423-5571 Lawrence Livermore National Laboratory, L-448 | Fax: (925) 422-2133 7000 East Ave., Livermore, CA 94550, USA | Bldg: 3751, Room: 109 *********************************************************************** From karplus@bray.cse.ucsc.edu Wed Jul 17 10:38:24 2002 Date: Wed, 17 Jul 2002 10:38:21 -0700 From: Kevin Karplus To: rost@columbia.edu CC: adamz@llnl.gov, volker@chem.columbia.edu, rachelk@soe.ucsc.edu, leszek@bioinfo.pl, learithe@soe.ucsc.edu, jcasper@soe.ucsc.edu, jmoult@tunc.org, karplus@soe.ucsc.edu In-reply-to: <3D3591B8.5040002@columbia.edu> (message from Burkhard Rost on Wed, 17 Jul 2002 11:48:08 -0400) Subject: Re: All 2ry predictions for SAM-T02 server rejected I would like to extend my thanks to everyone involved for coming up with a viable workaround for my error (thinking the CASP alphabet had been extended when it had not). I'm glad that all the predictions we made could be included in the CAFASP and CASP experiment, and that weveryone was so patient with me when it was obviously all my mistake. Kevin Karplus From leszek@bioinfo.pl Fri Jul 19 02:49:58 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Livebench@Bioinfo. Pl" Subject: CAFASP -> CASP Date: Fri, 19 Jul 2002 11:50:27 +0200 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear CAFASPers, The models that were sent to CASP already are indicated with black dates on http://bioinfo.pl/cafasp/3/. The rest will be sent later and is indicated with green dates. There are 3 targets with red dates and this indicates that the CASP pdb template files do not start with amino acid 1. Despite earlier promises CASP did not change their policy regarding the numbering of amino acids. This means of course that all our models have a wrong format in such cases. There are various ways we could deal with this problem: 1) Don't send such models to CASP. They would be evaluated in CAFASP but not in CASP. This has the advantage that we would create some pressure on CASP to change their (pointless in my opinion) numbering scheme. This has the disadvantage that the evaluation of servers in CASP would be compromised and the servers would get penalized due to missing models relative to human predictors. I expect that most of us (servers) would be interested to compete with human groups and this option will remain theoretical. 2) Send models as they are and all of us will have to renumber the models manually. I think pushing 50 research teams to work on changing thousands of numbers in many files is crazy but this option is default based on CASP-CAFASP negotiation results. 3) Write to CASP and ask them to renumber our models for their purpose. We, the CAFASP organizers, did this of course for weeks but failed to achieve any commitments. The current situation is that all models will be probably rejected by the CASP filter. Maybe the CAFASP community as a whole would be more convincing, but please don't tell them that I have suggested this :-). 4) We (or somebody) would write a script to renumber the models for everybody and we would try to incorporate it in the current set of submission scripts. This is of course a hazard. There will be little testing (there will be no CASP test submissions) and You may be flooded with error messages, because the formats our servers produce are far from uniformity. I will start working on option 4 next week and I hope I will not introduce too many errors in Your files. We could obviously discuss the options, but I admit that wasting the time of the scientific community with the problem of numbers in files is slightly ignorant. Best regards, Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl From David.Jones@cs.ucl.ac.uk Fri Jul 19 03:24:45 2002 MIME-Version: 1.0 Date: Fri, 19 Jul 2002 11:24:40 +0100 (BST) From: David Jones To: Leszek Rychlewski Cc: "Livebench@Bioinfo. Pl" Subject: Re: CAFASP -> CASP In-Reply-To: Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Leszek, I agree with you that the numbering issue with CASP entries is ridiculous. It's not as if the experimental structures which we eventually get are guaranteed to conform to the same numbering scheme - we all end up having to align the submissions with the experimental structures no matter what. In that case why not just start with residue 1 in all cases. On Fri, 19 Jul 2002, Leszek Rychlewski wrote: > > 2) Send models as they are and all of us will have to renumber the models > manually. I think pushing 50 research teams to work on changing thousands of > numbers in many files is crazy but this option is default based on > CASP-CAFASP negotiation results. Not that bad an option - certainly not as bad as last year when we had to do all the formatting for all our CAFASP/CASP submissions. > 4) We (or somebody) would write a script to renumber the models for > everybody and we would try to incorporate it in the current set of > submission scripts. This is of course a hazard. There will be little testing > (there will be no CASP test submissions) and You may be flooded with error > messages, because the formats our servers produce are far from uniformity. > > I will start working on option 4 next week and I hope I will not introduce > too many errors in Your files. We could obviously discuss the options, but I > admit that wasting the time of the scientific community with the problem of > numbers in files is slightly ignorant. There are a lot of PDB renumbering tools out there - I have a trivial one which just renumbers starting at a specified number. However, you might want to contact Andrew Martin, who was involved with the CASP2 comparative modelling assessment - his e-mail is a.c.r.martin@reading.ac.uk - he has several very nice tools for dealing with PDB renumbering - including one which ensures that the residue IDs across a whole set of PDB files are consistent with a master file. This might be just what you need. - David - > > Best regards, > > Leszek > > BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland > Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl > -- Professor David T. Jones | Email: David.Jones@cs.ucl.ac.uk Address: Bioinformatics Unit, | Direct Tel: +44 20 76797982 Dept. of Computer Science, | Lab Tel: +44 20 76797981 University College London, | Gower Street, London WC1E 6BT, U.K. | Fax: +44 20 73871397 From dfischer@cs.bgu.ac.il Fri Jul 19 05:15:32 2002 MIME-Version: 1.0 X-Authentication-Warning: lace.cs.bgu.ac.il: dfischer owned process doing -bs Date: Fri, 19 Jul 2002 15:15:22 +0300 (IDT) From: Daniel Fischer X-Sender: dfischer@lace To: Leszek Rychlewski Cc: "Livebench@Bioinfo. Pl" Subject: Re: CAFASP -> CASP In-Reply-To: Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Hi, Some experimental structures come with numbers not starting at 1, and casp probably prefers that hundreds of participants do the renumbering themselves rather than changing the template numbering, maybe to preserve the "experimental data integrity". I don't understand why this is, and I remember from previous casps how this numbering issue made the formatting difficult. We at CAFASP will use all models starting at one, exactly as they are generated by the servers, and those experimental structures that do not start at 1, we will renumber so they start at 1 and be consecutive. So, the only problem is to have the servers predictions pass the format requirements of casp, so that they are also evaluated by casp. I guess that casp won't want to renumber the models for us, so at the end each of us will have to renumber these models by hand (probably with the aid of some existing scripts?). In any case, I agree with D. Jones: the problem is much less severe than in last CAFASP, where each developer had to submit to casp their formatted models one by one. At least this time, thanks to Leszek's meta-server scripts, the vast majority of models are submitted to casp automatically and with no formatting problems. So far there are only about 3 or 4 such anomalous templates; hopefully there won't be many more... D On Fri, 19 Jul 2002, Leszek Rychlewski wrote: > Dear CAFASPers, > > The models that were sent to CASP already are indicated with black dates on > http://bioinfo.pl/cafasp/3/. The rest will be sent later and is indicated > with green dates. There are 3 targets with red dates and this indicates that > the CASP pdb template files do not start with amino acid 1. Despite earlier > promises CASP did not change their policy regarding the numbering of amino > acids. This means of course that all our models have a wrong format in such > cases. There are various ways we could deal with this problem: > > 1) Don't send such models to CASP. They would be evaluated in CAFASP but not > in CASP. This has the advantage that we would create some pressure on CASP > to change their (pointless in my opinion) numbering scheme. This has the > disadvantage that the evaluation of servers in CASP would be compromised and > the servers would get penalized due to missing models relative to human > predictors. I expect that most of us (servers) would be interested to > compete with human groups and this option will remain theoretical. > > 2) Send models as they are and all of us will have to renumber the models > manually. I think pushing 50 research teams to work on changing thousands of > numbers in many files is crazy but this option is default based on > CASP-CAFASP negotiation results. > > 3) Write to CASP and ask them to renumber our models for their purpose. We, > the CAFASP organizers, did this of course for weeks but failed to achieve > any commitments. The current situation is that all models will be probably > rejected by the CASP filter. Maybe the CAFASP community as a whole would be > more convincing, but please don't tell them that I have suggested this :-). > > 4) We (or somebody) would write a script to renumber the models for > everybodyand we would try to incorporate it in the current set of > submission scripts. This is of course a hazard. There will be little testing > (there will be no CASP test submissions) and You may be flooded with error > messages, because the formats our servers produce are far from uniformity. > > I will start working on option 4 next week and I hope I will not introduce > too many errors in Your files. We could obviously discuss the options, but I > admit that wasting the time of the scientific community with the problem of > numbers in files is slightly ignorant. > > Best regards, > > Leszek > > BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland > Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl > From ccamacho@tonka.bu.edu Fri Jul 19 07:29:39 2002 MIME-Version: 1.0 X-Authentication-Warning: lego.bu.edu: ccamacho owned process doing -bs Date: Fri, 19 Jul 2002 10:28:45 -0400 From: "Carlos J. Camacho" To: Leszek Rychlewski Cc: "Livebench@Bioinfo. Pl" Subject: Re: CAFASP -> CASP In-Reply-To: Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Dear Leszek, all: Should we expect an AUTOMATIC REPLY for ALL the submissions from CAFASP to CASP5 (Black dates on cafasp/3) ?? If I understand correctly, our submissions that do not model the first, say 10 residues, of a given target and therefore start with residue nr. 11, should be renumbered by substracting 10 from all the original residue numbers? Is this correct? Can I fix the submissions already in CASP5, or only CAFASP can do it ? Sincerely Carlos ******************************************* Carlos J. Camacho Research Assistant Professor Biomedical Engineering Boston University 44 Cummington St. Boston, MA 02215 Phone: (617) 353-4842 Fax: (617) 353-6766 ******************************************* From leszek@bioinfo.pl Sun Jul 21 10:48:34 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Livebench@Bioinfo. Pl" Subject: ugly CASP targets Date: Sun, 21 Jul 2002 19:48:49 +0200 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 (Normal) X-MSMail-Priority: Normal Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear CAFASPers I sent the results for targets 134 139 150, which have numbering irregularities. I hope I did not introduce a bug in the numbering. If all results will be wrong I will try to send them again (CASP will tell me). If not, You are asked to correct only the few wrong models which are not due to the numbering (CAFASP checks if the numbering in results corresponds to CAFASP targets and we notify You if not. All accepted and stored predictions at our site have thus correct CAFASP numbers). I hope there will be no other targets like this. Yours, Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl From bystrc@rpi.edu Mon Jul 22 09:16:13 2002 MIME-Version: 1.0 Date: Mon, 22 Jul 2002 12:16:07 -0400 From: Chris Bystroff Reply-To: bystrc@rpi.edu Organization: RPI X-Accept-Language: en,zh,es To: Leszek Rychlewski Cc: "Livebench@Bioinfo. Pl" Subject: Re: ugly CASP targets Content-Type: multipart/mixed; boundary="------------86E2FF88B560CEF706FDA862" X-Scanned-By: MIMEDefang 2.3 (www dot roaringpenguin dot com slash mimedefang) X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK This is a multi-part message in MIME format. --------------86E2FF88B560CEF706FDA862 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Leszek-- What do we do about rejected submissions from CAFASP to CASP? Could you send our server's results back to us when you send them to CASP? That way,we can edit them and resubmit. I hope they are still acceptable as "fully automatic" An alternative would be for Servers to accept a PDB template (more work for us...) --Chris Leszek Rychlewski wrote: > Dear CAFASPers > > I sent the results for targets 134 139 150, which have numbering > irregularities. I hope I did not introduce a bug in the numbering. If all > results will be wrong I will try to send them again (CASP will tell me). If > not, You are asked to correct only the few wrong models which are not due to > the numbering (CAFASP checks if the numbering in results corresponds to > CAFASP targets and we notify You if not. All accepted and stored predictions > at our site have thus correct CAFASP numbers). I hope there will be no other > targets like this. > > Yours, > > Leszek > > BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland > Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl --------------86E2FF88B560CEF706FDA862 Content-Type: text/x-vcard; charset=us-ascii; name="bystrc.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Chris Bystroff Content-Disposition: attachment; filename="bystrc.vcf" begin:vcard n:Bystroff;Chris tel;fax:518-276-2162 tel;work:518-276-3185 x-mozilla-html:TRUE url:http://isites.bio.rpi.edu/bystrc/index.html org:Rensselaer Polytechnic Institute;Biology version:2.1 email;internet:bystrc@rpi.edu title:Asst Professor note:Think Globally, Act Locally adr;quoted-printable:;;MRC 303=0D=0A110 8th St.;Troy;NY;12180;USA x-mozilla-cpt:;3 fn:Chris Bystroff end:vcard --------------86E2FF88B560CEF706FDA862-- From arne@sbc.su.se Mon Jul 22 12:58:40 2002 MIME-Version: 1.0 X-Original-Recipient: leszek@bioinfo.pl Content-Type: text/plain; charset="iso-8859-1" From: Arne Elofsson Reply-To: arne@sbc.su.se To: bystrc@rpi.edu, Leszek Rychlewski Subject: Re: ugly CASP targets Date: Mon, 22 Jul 2002 23:04:55 +0200 User-Agent: KMail/1.4.1 Cc: "Livebench@Bioinfo. Pl" In-Reply-To: <3D3C2FC8.43E67E82@rpi.edu> X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK On Monday 22 July 2002 18.16, Chris Bystroff wrote: > Leszek-- > What do we do about rejected submissions from CAFASP to CASP? > > Could you send our server's results back to us when you send them to CASP? > That way,we can edit them and resubmit. I hope they are still > acceptable as "fully automatic" > > An alternative would be for Servers to accept a PDB template (more work for > us...) So far I have had to use their manual correction scheme (quite omplicated but for a few targets (or actualla a few handfulls) it is managable. Some tips: 1) Check PARENT records (all my problesm was with the chain names) 2) upload template 3) Correct template and add PIN-code 4) If you need to make more corrections you should use the first PIN-code (and not the one is subsequent emails) yours arne From casp5@bialko.llnl.gov Tue Jul 23 11:08:26 2002 Date: Tue, 23 Jul 2002 11:08:20 -0700 (PDT) From: CASP5 To: karplus@soe.ucsc.edu Subject: CASP5: Prediction of disordered regions X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear CASP5 Predictor: A reminder that prediction of disordered regions is an official category in CASP5. See the web site for details. http://PredictionCenter.llnl.gov/casp5/doc/casp5-format.html CASP5 Organizers. From rost@columbia.edu Wed Jul 3 10:35:47 2002 MIME-Version: 1.0 Date: Wed, 03 Jul 2002 13:35:47 -0400 From: Burkhard Rost Reply-To: rost@columbia.edu Organization: Columbia University User-Agent: Mozilla/5.0 (Macintosh; U; PPC; en-US; rv:1.0.0) Gecko/20020529 X-Accept-Language: en-us, en To: Rachel Karchin CC: adamz@llnl.gov, leszek@bioinfo.pl, "Karplus,Kevin" , learithe@soe.ucsc.edu, jcasper@soe.ucsc.edu, "Eyrich,Volker" Subject: Re: All 2ry predictions for SAM-T02 server rejected Content-Type: text/plain; charset=us-ascii; format=flowed X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK my suggestion: just add group 4 (and give us a script that does the conversion of the old predictions) ... adam: what is yours? b Rachel Karchin wrote: > Dear Burkhard, Adam and Leszek: > > We've written the code to produce another secondary structure > prediction output just for CASP, which collapses the > richer local structure alphabets down to 3 states. > > Here are some questions: > > -- for CAFASP, when a request includes CaspResults=on, we currently > send out three emails of prediction results with these subject lines: > > o SAM_T02 CASP models (FR .al files) > o sam-t02-stride (stride-EBGHTL prediction) > o sam-t02-dssp (dssp-EBGHSTL prediction) > > I would like to add a fourth email of prediction results: > > o sam-t02-dssp-ehl > > This will be the three-state prediction in CASP format. > We'd like to continue to submit the full dssp and stride > predictions to EVA. > > Does this work for you? > > -- for CASP, we are registered as four "groups", three of > which are for automated predictions: > > > SAM-T02-server 5035-2079-5263 > SAM-T02-server-dssp 2491-6940-1261 > SAM-T02-server-stride 5144-8387-2760 > > but since they will not be evaluated for CASP, should we > discontinue SAM-T02-server-dssp and SAM-T02-server-stride? > > How does one discontinue a CASP group? > > Also, how do we register our new dssp-ehl group? Should we re-use > the SAM-T02-server-dssp membership for the new predictions? > > -- rk > > ------------------------------------------------------------------------- > Rachel Karchin > bioinformatics Ph.D. candidate > Office phone: (831) 459-5431 > http://www.cse.ucsc.edu/~rachelk > email: rachelk@cse.ucsc.edu > -- -------------------------------------------------------------- Burkhard Rost CUBIC, Columbia University tel +1-212-305 3773 Dept Biochemistry & Mol Biophysics fax +1-212-305 7932 630 West, 168 Street, BB 217 New York, N.Y. 10032 Mail: rost@columbia.edu WWW: http://www.columbia.edu/~rost/ http://cubic.bioc.columbia.edu/ http://www.c2b2.columbia.edu/ From adamz@llnl.gov Wed Jul 3 11:07:17 2002 MIME-Version: 1.0 Sender: adamz@bialko.llnl.gov Date: Wed, 03 Jul 2002 11:07:03 -0700 From: Adam ZEMLA Organization: Lawrence Livermore National Laboratory X-Accept-Language: en To: rost@columbia.edu CC: Rachel Karchin , leszek@bioinfo.pl, "Karplus,Kevin" , learithe@soe.ucsc.edu, jcasper@soe.ucsc.edu, "Eyrich,Volker" , jmoult@tunc.org Subject: Re: All 2ry predictions for SAM-T02 server rejected Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Burkhard Rost wrote: > > my suggestion: > just add group 4 (and give us a script that does the conversion > of the old predictions) ... > > adam: what is yours? > b Yes, it is fine with us. Rachel: please register your new sam-t02-dssp-ehl server for CASP and CAFASP, and send a script to Eyrich Volker. After the conversion will be done we will remove your two servers: SAM-T02-server-dssp and SAM-T02-server-stride from the CASP database, and as John said you will continue submit CASP formatted predictions under the new server ID. Thank you, Adam > > Rachel Karchin wrote: > > Dear Burkhard, Adam and Leszek: > > > > We've written the code to produce another secondary structure > > prediction output just for CASP, which collapses the > > richer local structure alphabets down to 3 states. > > > > Here are some questions: > > > > -- for CAFASP, when a request includes CaspResults=on, we currently > > send out three emails of prediction results with these subject lines: > > > > o SAM_T02 CASP models (FR .al files) > > o sam-t02-stride (stride-EBGHTL prediction) > > o sam-t02-dssp (dssp-EBGHSTL prediction) > > > > I would like to add a fourth email of prediction results: > > > > o sam-t02-dssp-ehl > > > > This will be the three-state prediction in CASP format. > > We'd like to continue to submit the full dssp and stride > > predictions to EVA. > > > > Does this work for you? > > > > -- for CASP, we are registered as four "groups", three of > > which are for automated predictions: > > > > > > SAM-T02-server 5035-2079-5263 > > SAM-T02-server-dssp 2491-6940-1261 > > SAM-T02-server-stride 5144-8387-2760 > > > > but since they will not be evaluated for CASP, should we > > discontinue SAM-T02-server-dssp and SAM-T02-server-stride? > > > > How does one discontinue a CASP group? > > > > Also, how do we register our new dssp-ehl group? Should we re-use > > the SAM-T02-server-dssp membership for the new predictions? > > > > -- rk > > > > ------------------------------------------------------------------------- > > Rachel Karchin > > bioinformatics Ph.D. candidate > > Office phone: (831) 459-5431 > > http://www.cse.ucsc.edu/~rachelk > > email: rachelk@cse.ucsc.edu > > > > -- > -------------------------------------------------------------- > Burkhard Rost > CUBIC, Columbia University tel +1-212-305 3773 > Dept Biochemistry & Mol Biophysics fax +1-212-305 7932 > 630 West, 168 Street, BB 217 > New York, N.Y. 10032 > Mail: rost@columbia.edu > WWW: http://www.columbia.edu/~rost/ > http://cubic.bioc.columbia.edu/ > http://www.c2b2.columbia.edu/ -- *********************************************************************** Adam Zemla, Ph.D. | E-mail: adamz@llnl.gov Biology and Biotechnology Research Program | Phone: (925) 423-5571 Lawrence Livermore National Laboratory, L-448 | Fax: (925) 422-2133 7000 East Ave., Livermore, CA 94550, USA | Bldg: 3751, Room: 109 *********************************************************************** From leszek@bioinfo.pl Tue Jul 9 05:46:48 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Livebench@Bioinfo. Pl" Subject: CAFASP models Date: Tue, 9 Jul 2002 14:46:56 +0200 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear CAFASPers, I would like to remind You that all models that were submitted until now to CASP are also at: http://bioinfo.pl/cafasp/3/output/ . Please contact me if You think I have missed any models. (only the models in TS format were actually sent, not the AL formatted ones) Yours, Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl From kaf@grot.llnl.gov Wed Jul 24 18:15:01 2002 Date: Wed, 24 Jul 2002 18:14:55 -0700 (PDT) From: Krzysztof Fidelis To: karplus@soe.ucsc.edu Subject: Appeal for prediction targets - a message from CASP president X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear CASP5 Predictor: We are now very well on with the CASP prediction season. As some of you will be aware, by historical standards we doing reasonably well with targets suitable for comparative modeling, but quite poorly with difficult fold recognition/new fold prediction ones. I had hoped that Structural Genomics activities would prove a good source for such targets, but that has turned out to be much harder to tap into than expected. So I am repeating the appeal I made earlier, but with considerably more desperation: We are asking that those of you who have contacts with experimentalists PLEASE talk to them, and persuade them to put in one or more targets. As always, information about the terms of target submission and release, and the submission form are at: http://predictioncenter.llnl.gov/casp5/targets/forms/casp5-tar.html We still need all sorts of prediction targets, but most particularly, the difficult fold recognition/new fold ones. These are exciting times in that prediction area, and it would be a great pity if CASP5 was not able to deliver a clear message about where the field has got to. Please get in touch if you have any questions or concerns. John Moult For CASP5 organizers. From karplus@bray.cse.ucsc.edu Fri Jul 26 08:36:08 2002 Date: Fri, 26 Jul 2002 08:36:04 -0700 From: Kevin Karplus To: leszek@bioinfo.pl CC: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu In-reply-to: Subject: Re: LiveBench If the SAM-T02 server is not in LiveBench, please add it. Also, I think the SAM-T02 server was broken for a while yesterday, due to an accidentally corrupted file. Please resubmit T0162 and T0163 to the server. From karplus@bray.cse.ucsc.edu Fri Jul 26 16:27:55 2002 Date: Fri, 26 Jul 2002 16:27:48 -0700 From: Kevin Karplus To: leszek@bioinfo.pl, dfischer@cs.bgu.ac.il CC: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu Subject: resubmit T0162 and T0163 Leszek, Did you get my message from earlier today asking that T0162 and T0163 be resubmitted to the SAM-T02 server? The server had a temporary glitch yesterday due to a corrupted file. Unfortunately, the targets were submitted while the server was misbehaving. I see that you have resubmitted T0163, and it is almost done, but I don't see T0162---please submit it without waiting for T0163 to finish. (Rachel---I think our server is generating FAR too many alignments for target T0163---there are 328 templates in the best-scores.rdb file---this will make the web server take a long time to finish the target.) Kevin From pdb-l-admin@SDSC.EDU Sat Jul 27 17:21:34 2002 From: Kevin Karplus To: pdb-l@rcsb.org Subject: pdb-l: prediction targets needed for CASP5 Sender: pdb-l-admin@SDSC.EDU X-BeenThere: pdb-l@sdsc.edu X-Mailman-Version: 2.0.8 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: The PDB mailing list List-Unsubscribe: , List-Archive: Date: Sat, 27 Jul 2002 17:06:45 -0700 I'm forwarding this message to the PDB-L list, in the hopes that some experimenters with nasty, hard-to-predict structures will help those of us in the prediction community embarass ourselves by predicting ludicrously wrong structures. Kevin Karplus Dear CASP5 Predictor: We are now very well on with the CASP prediction season. As some of you will be aware, by historical standards we doing reasonably well with targets suitable for comparative modeling, but quite poorly with difficult fold recognition/new fold prediction ones. I had hoped that Structural Genomics activities would prove a good source for such targets, but that has turned out to be much harder to tap into than expected. So I am repeating the appeal I made earlier, but with considerably more desperation: We are asking that those of you who have contacts with experimentalists PLEASE talk to them, and persuade them to put in one or more targets. As always, information about the terms of target submission and release, and the submission form are at: http://predictioncenter.llnl.gov/casp5/targets/forms/casp5-tar.html We still need all sorts of prediction targets, but most particularly, the difficult fold recognition/new fold ones. These are exciting times in that prediction area, and it would be a great pity if CASP5 was not able to deliver a clear message about where the field has got to. Please get in touch if you have any questions or concerns. John Moult For CASP5 organizers. From leszek@bioinfo.pl Sun Jul 28 06:09:07 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Kevin Karplus" , Cc: Subject: RE: resubmit T0162 and T0163 Date: Sun, 28 Jul 2002 15:09:30 +0200 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 In-Reply-To: <200207262327.g6QNRmW30515@bray.cse.ucsc.edu> X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Kevin, Please check again. I sent both targets few (60) minutes ago. If You want I can send them again after an hour (Don't worry about the deadline). Yours, Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl PS: the submission confirmation: Submission Confirmation Page
When your SAM_T02 build finishes, results will be available at
http://www.cse.ucsc.edu/research/compbio/SAM_T02 /results/target02-query-1027858212-15638/summary.html

You may wish to bookmark the above url for easy access to the results.

> -----Original Message----- > From: Kevin Karplus [mailto:karplus@soe.ucsc.edu] > Sent: Saturday, July 27, 2002 1:28 AM > To: leszek@bioinfo.pl; dfischer@cs.bgu.ac.il > Cc: karplus@soe.ucsc.edu; rachelk@soe.ucsc.edu > Subject: resubmit T0162 and T0163 > > > > Leszek, > > Did you get my message from earlier today asking that T0162 and T0163 > be resubmitted to the SAM-T02 server? The server had a temporary > glitch yesterday due to a corrupted file. Unfortunately, the targets > were submitted while the server was misbehaving. > > I see that you have resubmitted T0163, and it is almost done, but I > don't see T0162---please submit it without waiting for T0163 to finish. > > (Rachel---I think our server is generating FAR too many alignments for > target T0163---there are 328 templates in the best-scores.rdb > file---this will make the web server take a long time to finish the > target.) > > Kevin > From karplus@bray.cse.ucsc.edu Sun Jul 28 09:09:33 2002 Date: Sun, 28 Jul 2002 09:09:28 -0700 From: Kevin Karplus To: leszek@bioinfo.pl CC: dfischer@cs.bgu.ac.il, rachelk@soe.ucsc.edu, karplus@soe.ucsc.edu In-reply-to: Subject: Re: resubmit T0162 and T0163 It looks to me like both jobs started ok this morning, and one of them has finished already. I'll check again in a few hours to make sure that the other has finished also. Sorry about the extra trouble---we try to keep our server running, but we still have a few files that are shared between the development version and the installed version, so it is not quite as robust as we'd like. (At least the file system has been moved off of the failing server, so one of our major points of failure has been removed.) Kevin From karplus@bray.cse.ucsc.edu Sun Jul 28 09:13:22 2002 Date: Sun, 28 Jul 2002 09:13:20 -0700 From: Kevin Karplus To: fidelis@llnl.gov, adamz@llnl.gov Cc: karplus@soe.ucsc.edu Subject: server failure? I submitted T0135 twice yesterday, using the same procedure as I used for submitting T0132 on Friday. I got the T0132 acknowledgement back within minutes, but I got NO acknowledgement for T0135. Since T0135 has a deadline tomorrow, I would REALLY like to know what is going on, so that I can submit on time. Any help you can give me would be appreciated. Kevin Karplus From leszek@bioinfo.pl Sun Jul 28 16:52:59 2002 Return-Path: From: "Leszek Rychlewski" To: "Kevin Karplus" Cc: , Subject: RE: resubmit T0162 and T0163 Date: Sun, 28 Jul 2002 20:28:38 +0200 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal In-Reply-To: <200207281609.g6SG9Sb14818@bray.cse.ucsc.edu> Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK No problem, Yours, Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl > -----Original Message----- > From: Kevin Karplus [mailto:karplus@soe.ucsc.edu] > Sent: Sunday, July 28, 2002 6:09 PM > To: leszek@bioinfo.pl > Cc: dfischer@cs.bgu.ac.il; rachelk@soe.ucsc.edu; karplus@soe.ucsc.edu > Subject: Re: resubmit T0162 and T0163 > > > It looks to me like both jobs started ok this morning, and one of them > has finished already. I'll check again in a few hours to make sure > that the other has finished also. > > Sorry about the extra trouble---we try to keep our server running, but > we still have a few files that are shared between the development > version and the installed version, so it is not quite as robust as > we'd like. (At least the file system has been moved off of the > failing server, so one of our major points of failure has been removed.) > > Kevin > From adamz@llnl.gov Sun Jul 28 10:55:49 2002 Return-Path: Sender: adamz@zemla1-1.llnl.gov Date: Sun, 28 Jul 2002 10:56:30 -0700 From: Adam ZEMLA Organization: Lawrence Livermore National Laboratory X-Accept-Language: en To: karplus@bray.cse.ucsc.edu CC: fidelis@llnl.gov, karplus@soe.ucsc.edu, adamz@llnl.gov Subject: Re: server failure? Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK I've checked that all your Friday submissions (including T0132, T0135) went through the system without any problems. Sometimes during weekends we can have temporary power or network outages. As usually to check the status of submissions predictors are welcomed to use the "CASP5 model list viewer" facility: http://PredictionCenter.llnl.gov/casp5/Casp5.html http://PredictionCenter.llnl.gov/casp5/models/casp5-models.html If you see that your prediction was not processed by the system, please resubmit it. Your current status is below. Adam The current status of accepted models submitted by group: SAM-T02-human MODEL_INDEX PIN_NUMBER LEADER_CODE ACCEPTANCE DATE E-MAIL ADDRESS T0129SS001_1 PIN_123526_15892 4069-6308-1312 07/26/02 15:00:20 karplus@bray.cse.ucsc.edu T0130SS001_1 PIN_121517_15891 4069-6308-1312 07/26/02 15:00:06 karplus@bray.cse.ucsc.edu T0131SS001_1 PIN_124193_15893 4069-6308-1312 07/26/02 15:00:34 karplus@bray.cse.ucsc.edu T0132TS001_1 PIN_280233_16002 4069-6308-1312 07/26/02 18:08:06 karplus@bray.cse.ucsc.edu T0132SS001_1 PIN_172999_15913 4069-6308-1312 07/26/02 15:05:17 karplus@bray.cse.ucsc.edu T0133SS001_1 PIN_132903_15895 4069-6308-1312 07/26/02 15:01:02 karplus@bray.cse.ucsc.edu T0134SS001_1 PIN_133751_15896 4069-6308-1312 07/26/02 15:01:16 karplus@bray.cse.ucsc.edu T0135SS001_1 PIN_136671_15899 4069-6308-1312 07/26/02 15:01:58 karplus@bray.cse.ucsc.edu T0136SS001_1 PIN_156716_15905 4069-6308-1312 07/26/02 15:03:21 karplus@bray.cse.ucsc.edu T0137SS001_1 PIN_134098_15897 4069-6308-1312 07/26/02 15:01:30 karplus@bray.cse.ucsc.edu T0138SS001_1 PIN_125905_15894 4069-6308-1312 07/26/02 15:00:48 karplus@bray.cse.ucsc.edu T0139SS001_1 PIN_141843_15900 4069-6308-1312 07/26/02 15:02:12 karplus@bray.cse.ucsc.edu T0140SS001_1 PIN_173945_15914 4069-6308-1312 07/26/02 15:05:31 karplus@bray.cse.ucsc.edu T0141SS001_1 PIN_177499_15916 4069-6308-1312 07/26/02 15:05:59 karplus@bray.cse.ucsc.edu T0142SS001_1 PIN_176953_15915 4069-6308-1312 07/26/02 15:05:45 karplus@bray.cse.ucsc.edu T0143SS001_1 PIN_136246_15898 4069-6308-1312 07/26/02 15:01:44 karplus@bray.cse.ucsc.edu T0144SS001_1 PIN_186872_15920 4069-6308-1312 07/26/02 15:06:54 karplus@bray.cse.ucsc.edu T0145SS001_1 PIN_144441_15901 4069-6308-1312 07/26/02 15:02:26 karplus@bray.cse.ucsc.edu T0146SS001_1 PIN_153629_15904 4069-6308-1312 07/26/02 15:03:08 karplus@bray.cse.ucsc.edu T0147SS001_1 PIN_183322_15917 4069-6308-1312 07/26/02 15:06:12 karplus@bray.cse.ucsc.edu T0148SS001_1 PIN_145369_15902 4069-6308-1312 07/26/02 15:02:40 karplus@bray.cse.ucsc.edu T0149SS001_1 PIN_186785_15919 4069-6308-1312 07/26/02 15:06:40 karplus@bray.cse.ucsc.edu T0150SS001_1 PIN_183436_15918 4069-6308-1312 07/26/02 15:06:26 karplus@bray.cse.ucsc.edu T0151SS001_1 PIN_192201_15921 4069-6308-1312 07/26/02 15:07:08 karplus@bray.cse.ucsc.edu T0152SS001_1 PIN_147193_15903 4069-6308-1312 07/26/02 15:02:54 karplus@bray.cse.ucsc.edu T0153SS001_1 PIN_161598_15908 4069-6308-1312 07/26/02 15:04:03 karplus@bray.cse.ucsc.edu T0154SS001_1 PIN_194903_15922 4069-6308-1312 07/26/02 15:07:22 karplus@bray.cse.ucsc.edu T0155SS001_1 PIN_154703_15906 4069-6308-1312 07/26/02 15:03:36 karplus@bray.cse.ucsc.edu T0156SS001_1 PIN_163022_15909 4069-6308-1312 07/26/02 15:04:17 karplus@bray.cse.ucsc.edu T0157SS001_1 PIN_156049_15907 4069-6308-1312 07/26/02 15:03:49 karplus@bray.cse.ucsc.edu T0158SS001_1 PIN_196298_15923 4069-6308-1312 07/26/02 15:07:35 karplus@bray.cse.ucsc.edu T0159SS001_1 PIN_167592_15911 4069-6308-1312 07/26/02 15:04:49 karplus@bray.cse.ucsc.edu T0160SS001_1 PIN_164362_15910 4069-6308-1312 07/26/02 15:04:33 karplus@bray.cse.ucsc.edu T0161SS001_1 PIN_201625_15925 4069-6308-1312 07/26/02 15:08:03 karplus@bray.cse.ucsc.edu T0162SS001_1 PIN_172786_15912 4069-6308-1312 07/26/02 15:05:03 karplus@bray.cse.ucsc.edu T0163SS001_1 PIN_198149_15924 4069-6308-1312 07/26/02 15:07:49 karplus@bray.cse.ucsc.edu END of the list ------------------------------------------------- >From karplus@bray.cse.ucsc.edu Sun Jul 28 09:13:24 2002 Date: Sun, 28 Jul 2002 09:13:20 -0700 From: Kevin Karplus To: fidelis@llnl.gov, adamz@llnl.gov Cc: karplus@soe.ucsc.edu Subject: server failure? I submitted T0135 twice yesterday, using the same procedure as I used for submitting T0132 on Friday. I got the T0132 acknowledgement back within minutes, but I got NO acknowledgement for T0135. Since T0135 has a deadline tomorrow, I would REALLY like to know what is going on, so that I can submit on time. Any help you can give me would be appreciated. Kevin Karplus From karplus@cse.ucsc.edu Sun Jul 28 18:13:05 2002 Return-Path: Date: Sun, 28 Jul 2002 18:13:00 -0700 From: Kevin Karplus To: adamz@llnl.gov CC: fidelis@llnl.gov, karplus@cse.ucsc.edu In-reply-to: <3D44304E.8F5D264D@llnl.gov> (message from Adam ZEMLA on Sun, 28 Jul 2002 10:56:30 -0700) Subject: Re: server failure? The two T0135_TS submissions I sent yesterday are not on the list you sent me, nor are they on the current list from the web page. I can only assume that they were lost somewhere between my machine and yours, though T0132 got through on Friday, and I've had no evidence of mail blockage in other ways. I'll try again. From leszek@bioinfo.pl Mon Jul 29 04:19:01 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Kevin Karplus" Cc: Subject: RE: resubmit T0162 and T0163 Date: Mon, 29 Jul 2002 13:19:30 +0200 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal In-Reply-To: <200207262327.g6QNRmW30515@bray.cse.ucsc.edu> Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Kevin, Can You check target T0163 again ? I don't think I have received a result. Yours, Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl > -----Original Message----- > From: Kevin Karplus [mailto:karplus@soe.ucsc.edu] > Sent: Saturday, July 27, 2002 1:28 AM > To: leszek@bioinfo.pl; dfischer@cs.bgu.ac.il > Cc: karplus@soe.ucsc.edu; rachelk@soe.ucsc.edu > Subject: resubmit T0162 and T0163 > > > > Leszek, > > Did you get my message from earlier today asking that T0162 and T0163 > be resubmitted to the SAM-T02 server? The server had a temporary > glitch yesterday due to a corrupted file. Unfortunately, the targets > were submitted while the server was misbehaving. > > I see that you have resubmitted T0163, and it is almost done, but I > don't see T0162---please submit it without waiting for T0163 to finish. > > (Rachel---I think our server is generating FAR too many alignments for > target T0163---there are 328 templates in the best-scores.rdb > file---this will make the web server take a long time to finish the > target.) > > Kevin > From adamz@llnl.gov Sun Jul 28 10:55:41 2002 MIME-Version: 1.0 Return-Path: Sender: adamz@zemla1-1.llnl.gov Date: Sun, 28 Jul 2002 10:56:30 -0700 From: Adam ZEMLA Organization: Lawrence Livermore National Laboratory X-Accept-Language: en To: karplus@bray.cse.ucsc.edu CC: fidelis@llnl.gov, karplus@soe.ucsc.edu, adamz@llnl.gov Subject: Re: server failure? Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK I've checked that all your Friday submissions (including T0132, T0135) went through the system without any problems. Sometimes during weekends we can have temporary power or network outages. As usually to check the status of submissions predictors are welcomed to use the "CASP5 model list viewer" facility: http://PredictionCenter.llnl.gov/casp5/Casp5.html http://PredictionCenter.llnl.gov/casp5/models/casp5-models.html If you see that your prediction was not processed by the system, please resubmit it. Your current status is below. Adam The current status of accepted models submitted by group: SAM-T02-human MODEL_INDEX PIN_NUMBER LEADER_CODE ACCEPTANCE DATE E-MAIL ADDRESS T0129SS001_1 PIN_123526_15892 4069-6308-1312 07/26/02 15:00:20 karplus@bray.cse.ucsc.edu T0130SS001_1 PIN_121517_15891 4069-6308-1312 07/26/02 15:00:06 karplus@bray.cse.ucsc.edu T0131SS001_1 PIN_124193_15893 4069-6308-1312 07/26/02 15:00:34 karplus@bray.cse.ucsc.edu T0132TS001_1 PIN_280233_16002 4069-6308-1312 07/26/02 18:08:06 karplus@bray.cse.ucsc.edu T0132SS001_1 PIN_172999_15913 4069-6308-1312 07/26/02 15:05:17 karplus@bray.cse.ucsc.edu T0133SS001_1 PIN_132903_15895 4069-6308-1312 07/26/02 15:01:02 karplus@bray.cse.ucsc.edu T0134SS001_1 PIN_133751_15896 4069-6308-1312 07/26/02 15:01:16 karplus@bray.cse.ucsc.edu T0135SS001_1 PIN_136671_15899 4069-6308-1312 07/26/02 15:01:58 karplus@bray.cse.ucsc.edu T0136SS001_1 PIN_156716_15905 4069-6308-1312 07/26/02 15:03:21 karplus@bray.cse.ucsc.edu T0137SS001_1 PIN_134098_15897 4069-6308-1312 07/26/02 15:01:30 karplus@bray.cse.ucsc.edu T0138SS001_1 PIN_125905_15894 4069-6308-1312 07/26/02 15:00:48 karplus@bray.cse.ucsc.edu T0139SS001_1 PIN_141843_15900 4069-6308-1312 07/26/02 15:02:12 karplus@bray.cse.ucsc.edu T0140SS001_1 PIN_173945_15914 4069-6308-1312 07/26/02 15:05:31 karplus@bray.cse.ucsc.edu T0141SS001_1 PIN_177499_15916 4069-6308-1312 07/26/02 15:05:59 karplus@bray.cse.ucsc.edu T0142SS001_1 PIN_176953_15915 4069-6308-1312 07/26/02 15:05:45 karplus@bray.cse.ucsc.edu T0143SS001_1 PIN_136246_15898 4069-6308-1312 07/26/02 15:01:44 karplus@bray.cse.ucsc.edu T0144SS001_1 PIN_186872_15920 4069-6308-1312 07/26/02 15:06:54 karplus@bray.cse.ucsc.edu T0145SS001_1 PIN_144441_15901 4069-6308-1312 07/26/02 15:02:26 karplus@bray.cse.ucsc.edu T0146SS001_1 PIN_153629_15904 4069-6308-1312 07/26/02 15:03:08 karplus@bray.cse.ucsc.edu T0147SS001_1 PIN_183322_15917 4069-6308-1312 07/26/02 15:06:12 karplus@bray.cse.ucsc.edu T0148SS001_1 PIN_145369_15902 4069-6308-1312 07/26/02 15:02:40 karplus@bray.cse.ucsc.edu T0149SS001_1 PIN_186785_15919 4069-6308-1312 07/26/02 15:06:40 karplus@bray.cse.ucsc.edu T0150SS001_1 PIN_183436_15918 4069-6308-1312 07/26/02 15:06:26 karplus@bray.cse.ucsc.edu T0151SS001_1 PIN_192201_15921 4069-6308-1312 07/26/02 15:07:08 karplus@bray.cse.ucsc.edu T0152SS001_1 PIN_147193_15903 4069-6308-1312 07/26/02 15:02:54 karplus@bray.cse.ucsc.edu T0153SS001_1 PIN_161598_15908 4069-6308-1312 07/26/02 15:04:03 karplus@bray.cse.ucsc.edu T0154SS001_1 PIN_194903_15922 4069-6308-1312 07/26/02 15:07:22 karplus@bray.cse.ucsc.edu T0155SS001_1 PIN_154703_15906 4069-6308-1312 07/26/02 15:03:36 karplus@bray.cse.ucsc.edu T0156SS001_1 PIN_163022_15909 4069-6308-1312 07/26/02 15:04:17 karplus@bray.cse.ucsc.edu T0157SS001_1 PIN_156049_15907 4069-6308-1312 07/26/02 15:03:49 karplus@bray.cse.ucsc.edu T0158SS001_1 PIN_196298_15923 4069-6308-1312 07/26/02 15:07:35 karplus@bray.cse.ucsc.edu T0159SS001_1 PIN_167592_15911 4069-6308-1312 07/26/02 15:04:49 karplus@bray.cse.ucsc.edu T0160SS001_1 PIN_164362_15910 4069-6308-1312 07/26/02 15:04:33 karplus@bray.cse.ucsc.edu T0161SS001_1 PIN_201625_15925 4069-6308-1312 07/26/02 15:08:03 karplus@bray.cse.ucsc.edu T0162SS001_1 PIN_172786_15912 4069-6308-1312 07/26/02 15:05:03 karplus@bray.cse.ucsc.edu T0163SS001_1 PIN_198149_15924 4069-6308-1312 07/26/02 15:07:49 karplus@bray.cse.ucsc.edu END of the list ------------------------------------------------- >From karplus@bray.cse.ucsc.edu Sun Jul 28 09:13:24 2002 Date: Sun, 28 Jul 2002 09:13:20 -0700 From: Kevin Karplus To: fidelis@llnl.gov, adamz@llnl.gov Cc: karplus@soe.ucsc.edu Subject: server failure? I submitted T0135 twice yesterday, using the same procedure as I used for submitting T0132 on Friday. I got the T0132 acknowledgement back within minutes, but I got NO acknowledgement for T0135. Since T0135 has a deadline tomorrow, I would REALLY like to know what is going on, so that I can submit on time. Any help you can give me would be appreciated. Kevin Karplus From karplus@bray.cse.ucsc.edu Mon Jul 29 08:44:09 2002 Date: Mon, 29 Jul 2002 08:44:54 -0700 From: Kevin Karplus To: leszek@bioinfo.pl CC: rachelk@soe.ucsc.edu, karplus@soe.ucsc.edu In-reply-to: Subject: Re: resubmit T0162 and T0163 We had a power outage yesterday that killed the machines that our server runs on. Our tech staff don't work weekends, so nothing came back up until today. Our power situation on campus is like a third-world country---we get at least a dozen outages a year, often more. I edited the "Makefile.core" file so that the server would not try to generate quite so many alignments (which are mostly not needed for the CASP predictions anyway), and things should run a little faster. Please resubmit T0163 once more, and let's keep our fingers crossed that we don't have another software or hardware failure. Kevin Karplus From leszek@bioinfo.pl Mon Jul 29 10:17:01 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Kevin Karplus" Cc: "Rachelk@Soe. Ucsc. Edu" Subject: RE: resubmit T0162 and T0163 Date: Mon, 29 Jul 2002 19:17:19 +0200 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal In-Reply-To: <200207291544.g6TFisO01577@bray.cse.ucsc.edu> Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Done It seems to by busy now. Yours, Leszek > -----Original Message----- > From: Kevin Karplus [mailto:karplus@soe.ucsc.edu] > Sent: Monday, July 29, 2002 5:45 PM > To: leszek@bioinfo.pl > Cc: rachelk@soe.ucsc.edu; karplus@soe.ucsc.edu > Subject: Re: resubmit T0162 and T0163 > > > We had a power outage yesterday that killed the machines that our > server runs on. Our tech staff don't work weekends, so nothing came > back up until today. Our power situation on campus is like a > third-world country---we get at least a dozen outages a year, often more. > > I edited the "Makefile.core" file so that the server would not try to > generate quite so many alignments (which are mostly not needed > for the CASP > predictions anyway), and things should run a little faster. > > Please resubmit T0163 once more, and let's keep our fingers crossed > that we don't have another software or hardware failure. > > Kevin Karplus > From leszek@bioinfo.pl Mon Jul 29 14:49:57 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Kevin Karplus" , "Rachelk@Soe. Ucsc. Edu" Subject: FW: SAM_T02 query failure Date: Mon, 29 Jul 2002 23:50:23 +0200 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0000_01C2375A.B4838E20" X-Priority: 3 (Normal) X-MSMail-Priority: Normal Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK This is a multi-part message in MIME format. ------=_NextPart_000_0000_01C2375A.B4838E20 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 7bit I sent T0164 again. Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl ------=_NextPart_000_0000_01C2375A.B4838E20 Content-Type: message/rfc822 Content-Transfer-Encoding: 7bit Content-Disposition: attachment From: To: Subject: SAM_T02 query failure Date: Mon, 29 Jul 2002 23:46:50 +0200 Message-ID: <200207292146.OAA20550@web01.cse.ucsc.edu> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 SAM_T02 experienced problems processing your query. Please try again. ------=_NextPart_000_0000_01C2375A.B4838E20-- From rachelk@roar.cse.ucsc.edu Mon Jul 29 14:59:07 2002 MIME-Version: 1.0 From: Rachel Karchin Content-Type: text/plain; charset=us-ascii Date: Mon, 29 Jul 2002 14:59:08 -0700 To: "Leszek Rychlewski" CC: karplus@soe.ucsc.edu Subject: Re: FW: SAM_T02 query failure In-Reply-To: X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Hi Leszek: Much to our frustration, we continue to have system problems today and our main system administrator is away on vacation. It looks like one of the filesystems filled up and I just deleted a bunch of temporary files. I think if you resubmit, the SAM_T02 query will be processed normally. Please let me know immediately if you get another error. -- rk ------------------------------------------------------------------------- Rachel Karchin bioinformatics Ph.D. candidate Office phone: (831) 459-5431 http://www.cse.ucsc.edu/~rachelk email: rachelk@cse.ucsc.edu Leszek Rychlewski writes: > I sent T0164 again. > > Leszek > > BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland > Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl > > From: > To: > Subject: SAM_T02 query failure > Date: Mon, 29 Jul 2002 23:46:50 +0200 > Message-ID: <200207292146.OAA20550@web01.cse.ucsc.edu> > MIME-Version: 1.0 > Content-Type: text/plain; > charset="iso-8859-1" > Content-Transfer-Encoding: 7bit > X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) > X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 > > SAM_T02 experienced problems processing your query. > > Please try again. From leszek@bioinfo.pl Mon Jul 29 15:05:07 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Rachel Karchin" Cc: Subject: RE: FW: SAM_T02 query failure Date: Tue, 30 Jul 2002 00:05:32 +0200 Content-Type: text/plain; charset="Windows-1252" X-Priority: 3 (Normal) X-MSMail-Priority: Normal In-Reply-To: <15685.47788.521695.779005@roar.cse.ucsc.edu> Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Rachel, No errors yet, but if this continues, can You just run the target Yourself and send the results to the meta server address samt02.8483@cyborg.bioinfo.pl (or to me). Yours, Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl > -----Original Message----- > From: Rachel Karchin [mailto:rachelk@soe.ucsc.edu] > Sent: Monday, July 29, 2002 11:59 PM > To: Leszek Rychlewski > Cc: karplus@soe.ucsc.edu > Subject: Re: FW: SAM_T02 query failure > > > Hi Leszek: > > Much to our frustration, we continue to have system problems today > and our main system administrator is away on vacation. > > It looks like one of the filesystems filled up and I just deleted > a bunch of temporary files. > > I think if you resubmit, the SAM_T02 query will be processed > normally. > > Please let me know immediately if you get another error. > > -- rk > > > ------------------------------------------------------------------------- > Rachel Karchin > bioinformatics Ph.D. candidate > Office phone: (831) 459-5431 > http://www.cse.ucsc.edu/~rachelk > email: rachelk@cse.ucsc.edu > > > > Leszek Rychlewski writes: > > I sent T0164 again. > > > > Leszek > > > > BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland > > Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl > > > > From: > > To: > > Subject: SAM_T02 query failure > > Date: Mon, 29 Jul 2002 23:46:50 +0200 > > Message-ID: <200207292146.OAA20550@web01.cse.ucsc.edu> > > MIME-Version: 1.0 > > Content-Type: text/plain; > > charset="iso-8859-1" > > Content-Transfer-Encoding: 7bit > > X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) > > X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 > > > > SAM_T02 experienced problems processing your query. > > > > Please try again. > > From rachelk@roar.cse.ucsc.edu Mon Jul 29 15:10:59 2002 MIME-Version: 1.0 From: Rachel Karchin Content-Type: text/plain; charset=us-ascii Date: Mon, 29 Jul 2002 15:11:01 -0700 To: "Leszek Rychlewski" CC: karplus@soe.ucsc.edu Subject: RE: FW: SAM_T02 query failure In-Reply-To: X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Of course. Let me know if there is another failure and I will run the target myself. -- rk ------------------------------------------------------------------------- Rachel Karchin bioinformatics Ph.D. candidate Office phone: (831) 459-5431 http://www.cse.ucsc.edu/~rachelk email: rachelk@cse.ucsc.edu > Rachel, > > No errors yet, but if this continues, can You just run the target Yourself > and send the results to the meta server address > samt02.8483@cyborg.bioinfo.pl (or to me). > > Yours, > > Leszek > > BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland > Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl > From leszek@bioinfo.pl Mon Jul 29 15:12:09 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Rachel Karchin" Cc: Subject: RE: FW: SAM_T02 query failure Date: Tue, 30 Jul 2002 00:12:34 +0200 Content-Type: text/plain; charset="Windows-1252" X-Priority: 3 (Normal) X-MSMail-Priority: Normal In-Reply-To: <15685.48501.633330.736876@roar.cse.ucsc.edu> Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK No error yet. I will check it again tomorrow. Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl > -----Original Message----- > From: Rachel Karchin [mailto:rachelk@soe.ucsc.edu] > Sent: Tuesday, July 30, 2002 12:11 AM > To: Leszek Rychlewski > Cc: karplus@soe.ucsc.edu > Subject: RE: FW: SAM_T02 query failure > > > Of course. Let me know if there is another failure and I will > run the target myself. > > -- rk > > > ------------------------------------------------------------------------- > Rachel Karchin > bioinformatics Ph.D. candidate > Office phone: (831) 459-5431 > http://www.cse.ucsc.edu/~rachelk > email: rachelk@cse.ucsc.edu > > > > Rachel, > > > > No errors yet, but if this continues, can You just run the > target Yourself > > and send the results to the meta server address > > samt02.8483@cyborg.bioinfo.pl (or to me). > > > > Yours, > > > > Leszek > > > > BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland > > Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl > > > > From leszek@bioinfo.pl Mon Jul 29 15:22:04 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Rachelk@Soe. Ucsc. Edu" , "Kevin Karplus" Subject: FW: SAM_T02 query failure Date: Tue, 30 Jul 2002 00:22:29 +0200 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0004_01C2375F.30A47420" X-Priority: 3 (Normal) X-MSMail-Priority: Normal Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK This is a multi-part message in MIME format. ------=_NextPart_000_0004_01C2375F.30A47420 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 7bit I got the error ! Please run it. Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl ------=_NextPart_000_0004_01C2375F.30A47420 Content-Type: message/rfc822 Content-Transfer-Encoding: 7bit Content-Disposition: attachment From: To: Subject: SAM_T02 query failure Date: Tue, 30 Jul 2002 00:19:32 +0200 Message-ID: <200207292219.PAA20933@web01.cse.ucsc.edu> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 SAM_T02 experienced problems processing your query. Please try again. ------=_NextPart_000_0004_01C2375F.30A47420-- From karplus@bark.cse.ucsc.edu Mon Aug 5 21:50:31 2002 Date: Mon, 5 Aug 2002 21:50:27 -0700 From: Kevin Karplus To: leszek@bioinfo.pl CC: stu@soe.ucsc.edu, rachelk@soe.ucsc.edu, karplus@soe.ucsc.edu Subject: SAMT-T99 for T0165 ... The meta-server says that SAM-T99 is "busy" for T0165, but there is no farmer job running that could correspond to that request. I submitted a small job to the SAM-T99 site that seemed to run just fine and sent me back e-mail. Leszek, please resubmit t0165, t0166, and t0167 to SAM-T99---I've no idea why you did not get results back already. t0166 has neither SAM-T99 nor SAM-T02 results, but I see SAM-T02 still running on it and should be done soon, so I think that the SAM-T02 server is running ok. I see no mention of SAM-T02 on the t0167 CAFASP page---perhaps the meta-server is waiting for t0166 to finish?? From casp5@bialko.llnl.gov Thu Aug 8 12:01:04 2002 Date: Thu, 8 Aug 2002 12:00:58 -0700 (PDT) From: CASP5 To: karplus@soe.ucsc.edu Subject: Message to CASP/CAFASP participants X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Dear CASP5 Participant: As you know, the CASP5 experiment is now well under way. The purpose of this message is to provide some updates. Targets: You may have noticed that the rate of new target release has increased lately. As usual, it has not been easy to generate enough prediction targets. In the last week or two, several structural genomics centers have started to help. Most of the targets now being released are from that source. We expect to release the last one around mid-August. (The rate of release is limited by the constraints of the CAFASP experiment). Prediction season: Because of the relative flood of late targets, we are extending the prediction season. The last targets will close in mid-September. Assessors: Following input from the consultancy groups, the three assessors have now been appointed. They are Anna Tramontano for comparative modeling, Nick Grishin for fold recognition and Rob Russell for new Fold methods. Refinement targets: As outlined in the CASP5 experiment prediction, selected comparative modeling predictions for closed targets will be provided as starting points for structure refinement experiments. Because of the need to use closed targets, the refinement experiment will run on beyond the main CASP experiment. Details will be follow shortly. Pittsburgh Supercomputing Center Resources: The computing time available at the PSC has not all been allocated. We hope that people may take advantage of it for the refinement experiment. See the CASP5 web page for details on how to apply. CASP5 Meeting: The CASP5 meeting will take place in Asilomar, December 1 5th. Registration for the meeting (which is separate from registration for CASP) will open in mid-August and close in mid-September. If you plan to attend, it is important to register early, as we have a record number of participants in CASP5, and space is limited. Preference will be given to active prediction group members, and early registrants. CAFASP/CASP interactions: As those of you taking part in CAFASP know, all CAFASP predictions are forwarded to become automatic server entries in CASP. The 'automatic' part of that is working reasonably well - 95% of forwarded CAFASP predictions are in CASP. That leaves 5% of problems, however. Submitters of all those cases should have received emails from the Livermore prediction center, describing the problem. We understand that fixing the formatting issues involved is a nuisance, and apologize for the inconvenience. But - to avoid disappointments later on - a gentle reminder that predictions that are not accepted at CASP will be removed from CAFASP. The deadline for correcting submissions is the CASP expiry date of each target. You can double check the status of your CAFASP -> CASP transitions on the Livermore site. John Moult For CASP5 organizers. From karplus@bray.cse.ucsc.edu Mon Aug 12 11:52:12 2002 Date: Mon, 12 Aug 2002 11:52:05 -0700 From: Kevin Karplus To: leszek@bioinfo.pl, dfischer@cs.bgu.ac.il CC: karplus@soe.ucsc.edu Subject: missing models I was just checking the CASP5 model-list viewer and saw some missing models: For SAM-T99 there are no TS models for T0135, though all other targets through T0158 seem to have been submitted. I was going to ask you to resubmit these models from the cached results, but I don't see SAM-T99 results on the bioinfo.pl/Meta page, though there are SAM-T99 secondary results. Since you don't have the results, there is no way they can be submitted now, so I guess SAM-T99 just loses out on this target (oh, well, it was a hard target so SAM-T99 would probably have done something ridiculous anyway). For SAM-T2K (tertiary) all targets through T0158 seem to have been submitted For SAM-T2K-dssp-ehl and SAM-T99 (secondary) all 2ry targets through T0176 seem to have been submitted So, it looks like there are no problems that need attention, though at first I thought there were. From leszek@bioinfo.pl Tue Aug 13 07:16:40 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Kevin Karplus" , Subject: RE: missing models Date: Tue, 13 Aug 2002 16:17:06 +0200 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal In-Reply-To: <200208121852.g7CIq5p27673@bray.cse.ucsc.edu> X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Kevin, Sam-T99 reported no hits for this target: http://bioinfo.pl/Meta/3djury.pl?id=7446&file=samt99 Unless this is a technical error the status of Sam-T submissions should be ok. Yours, Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl > -----Original Message----- > From: Kevin Karplus [mailto:karplus@soe.ucsc.edu] > Sent: Monday, August 12, 2002 8:52 PM > To: leszek@bioinfo.pl; dfischer@cs.bgu.ac.il > Cc: karplus@soe.ucsc.edu > Subject: missing models > > > > I was just checking the CASP5 model-list viewer and saw some > missing models: > > For SAM-T99 there are no TS models for T0135, though all other targets > through T0158 seem to have been submitted. > > I was going to ask you to resubmit these models from the cached > results, but I don't see SAM-T99 results on the bioinfo.pl/Meta page, > though there are SAM-T99 secondary results. Since you don't have the > results, there is no way they can be submitted now, so I guess SAM-T99 > just loses out on this target (oh, well, it was a hard target so > SAM-T99 would probably have done something ridiculous anyway). > > For SAM-T2K (tertiary) > all targets through T0158 seem to have been submitted > > For SAM-T2K-dssp-ehl and SAM-T99 (secondary) > all 2ry targets through T0176 seem to have been submitted > > > So, it looks like there are no problems that need attention, though at > first I thought there were. > From leszek@bioinfo.pl Tue Aug 13 07:21:39 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Livebench@Bioinfo. Pl" Subject: CAFASP targets 165,166,167 Date: Tue, 13 Aug 2002 16:22:06 +0200 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear CAFASPers, Due to technical reasons I have submitted targets T0165, T0166 and T0167 to CASP. Targets T0158 - T0164 will be sent soon. Yours Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl From karplus@bray.cse.ucsc.edu Tue Aug 13 07:41:59 2002 Date: Tue, 13 Aug 2002 07:41:57 -0700 From: Kevin Karplus To: leszek@bioinfo.pl CC: dfischer@cs.bgu.ac.il, karplus@soe.ucsc.edu In-reply-to: Subject: Re: missing models Given the difficulty of T0135, it was probably correct for SAM-T99 to report no hits. I had forgotten that it had a cutoff (SAM-T02 always tries to report SOMETHING). In fact, now that I think about it, I'm surprised that T0135 was the ONLY target that was cut off---SAM-T99 must have had a pretty generous threshold. Incidentally, I was looking at the new first-week Livebench results, and was disappointed in the performance of ST02---at first I couldn't figure out why we had missed 1jw3A, which even BLAST had found. It turned out that 1jw3A was not in our template library, because the FSSP FTP site (which we had been relying on to get representative sequences for NMR models) has not been updated since last October! I've updated our library using the FSSP web site (which is more current), and will try not to let our template library get so far behind again. Library currency is getting to be a bigger problem---we were relying on PDBAA from NCBI, and found (for T0177) that it did not include 1konA, even though PDB had had it out for 2 weeks. I'm not complaining about the LiveBench experiment---indeed I regard it as a GOOD thing that the test depends on library currency as well as technique, but I'm a bit miffed that I didn't fix the library problem BEFORE it affected sam-t02's standing. Oh well, I just hope that there are enough targets in the next few weeks for SAM-T02 to recover. Kevin From karplus@bray.cse.ucsc.edu Tue Aug 13 08:59:28 2002 Date: Tue, 13 Aug 2002 08:59:21 -0700 From: Kevin Karplus To: leszek@bioinfo.pl, dfischer@cs.bgu.ac.il CC: karplus@soe.ucsc.edu Subject: T0166 samt02.pdb 2 bad model I got warnings from CASP5 that PIN_252044_21649 T0166TS189_2 does not have complete main chain atoms, but the template it is based on (1BI0) does seem to be complete, so why are only CA atoms being sent? From leszek@bioinfo.pl Tue Aug 13 09:01:56 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Kevin Karplus" , Subject: RE: T0166 samt02.pdb 2 bad model Date: Tue, 13 Aug 2002 18:02:19 +0200 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal In-Reply-To: <200208131559.g7DFxLK14424@bray.cse.ucsc.edu> X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK This is based on a procedure negotiated with CASP. We will send only Calpha atoms for all servers (that return AL format). Please ignore it. Yours, Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl > -----Original Message----- > From: Kevin Karplus [mailto:karplus@soe.ucsc.edu] > Sent: Tuesday, August 13, 2002 5:59 PM > To: leszek@bioinfo.pl; dfischer@cs.bgu.ac.il > Cc: karplus@soe.ucsc.edu > Subject: T0166 samt02.pdb 2 bad model > > > > I got warnings from CASP5 that > PIN_252044_21649 T0166TS189_2 > does not have complete main chain atoms, but the template it is based > on (1BI0) does seem to be complete, so why are only CA atoms being sent? > From karplus@bray.cse.ucsc.edu Tue Aug 13 09:05:23 2002 Date: Tue, 13 Aug 2002 09:05:18 -0700 From: Kevin Karplus To: leszek@bioinfo.pl, dfischer@cs.bgu.ac.il CC: karplus@soe.ucsc.edu Subject: All CA-only Looking back over the acknowledgements, it seems that ALL of the CAFASP models translated from alignments are being sent as CA-only, so I suppose this was a deliberate decision. It might have been better to send just the alignments, since the CASP5 folks will include the whole backbone when THEY do the translations. Why are only the CA being sent? i must have missed that discussion. kevin From leszek@bioinfo.pl Tue Aug 13 09:29:03 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Kevin Karplus" , Subject: RE: All CA-only Date: Tue, 13 Aug 2002 18:29:26 +0200 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal In-Reply-To: <200208131605.g7DG5II14522@bray.cse.ucsc.edu> X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Casp wanted us to send only one format (not AL and TS, which we were sending at the beginning). The reason the send Calpha only is that in CAFASP we evaluated only Calphas, and I did not have the scripts for generating all backbone atoms. I don't think the warning is meaningful. CASP will also manage to evaluate the models when only Caplha atoms were submitted. (There was no discussion of this in our CAFASP group. On the other hand the negotiations with CASP took many weeks and I am not very happy about the results). Yours, Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl > -----Original Message----- > From: Kevin Karplus [mailto:karplus@soe.ucsc.edu] > Sent: Tuesday, August 13, 2002 6:05 PM > To: leszek@bioinfo.pl; dfischer@cs.bgu.ac.il > Cc: karplus@soe.ucsc.edu > Subject: All CA-only > > > > Looking back over the acknowledgements, it seems that ALL of the > CAFASP models translated from alignments are being sent as CA-only, so > I suppose this was a deliberate decision. > > It might have been better to send just the alignments, since the CASP5 > folks will include the whole backbone when THEY do the translations. > > Why are only the CA being sent? i must have missed that discussion. > > kevin > From leszek@bioinfo.pl Fri Aug 16 09:25:34 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Livebench@Bioinfo. Pl" Subject: T0173 Date: Fri, 16 Aug 2002 18:26:02 +0200 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear all, Because we had to change the target T0173 in our system (due to an error in the sequence) it was submitted by the system twice to CASP. I am truly sorry for the inconvenience. The second submission has overwritten Your corrections if You made any. Please send the corrections for target T0173 to CASP again. Sincerely, Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl From karplus@bray.cse.ucsc.edu Fri Aug 16 16:18:49 2002 Date: Fri, 16 Aug 2002 16:18:42 -0700 From: Kevin Karplus To: casp5@bialko.llnl.gov, jmoult@tunc.org, fidelis@llnl.gov, adamz@llnl.gov, th@sanger.ac.uk CC: karplus@soe.ucsc.edu Subject: Target T0139 published before deadline I just found out yesterday that T0139's structure was published a week ago Solution Structure of the DFF-C Domain of DFF45/ICAD. A Structural Basis for the Regulation of Apoptotic DNA Fragmentation. JMB 311:317-327 (2002) http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12144788&dopt=Abstract I wonder whether this means that the target should be removed from CASP5. I looked at the paper and tried to improve my predictions based on it, but I had very little time. I suspect that some other predictors may have had the full week to look at pictures of the correct structure, and others won't have seen it at all. Hardly a level playing field. Kevin Karplus From karplus@bray.cse.ucsc.edu Sun Aug 18 18:51:46 2002 Date: Sun, 18 Aug 2002 18:51:40 -0700 From: Kevin Karplus To: casp5@bialko.llnl.gov, jmoult@tunc.org, fidelis@llnl.gov, adamz@llnl.gov, th@sanger.ac.uk CC: karplus@soe.ucsc.edu Subject: 2nd Biennial Symposium on Bioinformatics at UCSC Please forward this message to all CASP5 predictors: Following the success of our first symposium on bioinformatics after CASP4, the University of California, Santa Cruz is hosting another one after CASP5 on Saturday and Sunday Dec 7-8, 2002. Full information can be found on the web at http://www.soe.ucsc.edu/research/compbio/workshop-2002.html Thank you, Kevin Karplus From leszek@bioinfo.pl Mon Aug 19 10:42:22 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Kevin Karplus" Subject: T0178 Date: Mon, 19 Aug 2002 19:42:48 +0200 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 (Normal) X-MSMail-Priority: Normal Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Kevin, Can You check what happened to SamT02 for target T0178 and send me the prediction ? Yours, Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl From karplus@bray.cse.ucsc.edu Mon Aug 19 11:01:32 2002 Date: Mon, 19 Aug 2002 11:01:27 -0700 From: Kevin Karplus To: leszek@bioinfo.pl CC: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu In-reply-to: Subject: Re: T0178 You asked me to fin dout what had happened to the SAMT02 run for target T0178. I found the run for T0178 in http://www.soe.ucsc.edu/research/compbio/SAM_T02/results/target02-query-1029181204-29070/ (It would be easier to find them if CAFASP used the CASP target numbers instead of making up the internal "fp" numbers---I had to go to the CAFASP site to get the fp number, then look for that in the log file.) Unfortunately, that run did not finish. As near as I can tell it died in the middle of running the template library. I suspect that the problem may have been that the template library was last updated 12 Aug 14:07, and the query died 12 Aug 14:08---the library was updated just as the query was using it, and there is no concurrency control to check this. If you had resubmitted the sequence after the failure, it should have run just fine, as the error is one that will not recur frequently. Since the run did not finish, the only way to get results would be to rerun it. I believe you did get the secondary-structure results, which are mailed before the fold-recognition is done and thus before the failure ocurred. From leszek@bioinfo.pl Mon Aug 19 11:04:30 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Kevin Karplus" Cc: Subject: RE: T0178 Date: Mon, 19 Aug 2002 20:04:56 +0200 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal Importance: Normal In-Reply-To: <200208191801.g7JI1RY15774@bray.cse.ucsc.edu> X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK I will try to rerun it. Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl > -----Original Message----- > From: Kevin Karplus [mailto:karplus@soe.ucsc.edu] > Sent: Monday, August 19, 2002 8:01 PM > To: leszek@bioinfo.pl > Cc: karplus@soe.ucsc.edu; rachelk@soe.ucsc.edu > Subject: Re: T0178 > > > You asked me to fin dout what had happened to the SAMT02 run for > target T0178. > > I found the run for T0178 in > > http://www.soe.ucsc.edu/research/compbio/SAM_T02/results/target02- > query-1029181204-29070/ > (It would be easier to find them if CAFASP used the CASP target numbers > instead of making up the internal "fp" numbers---I had to go to the > CAFASP site to get the fp number, then look for that in the log file.) > > Unfortunately, that run did not finish. As near as I can tell it > died in the middle of running the template library. I suspect that > the problem may have been that the template library was last updated > 12 Aug 14:07, and the query died 12 Aug 14:08---the library was > updated just as the query was using it, and there is no concurrency > control to check this. > > If you had resubmitted the sequence after the failure, it should have > run just fine, as the error is one that will not recur frequently. > > Since the run did not finish, the only way to get results would be to > rerun it. I believe you did get the secondary-structure results, > which are mailed before the fold-recognition is done and thus before > the failure ocurred. > From leszek@bioinfo.pl Tue Aug 20 01:45:31 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Livebench@Bioinfo. Pl" Subject: 2nd Biennial Symposium on Bioinformatics at UCSC Date: Tue, 20 Aug 2002 10:46:01 +0200 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 (Normal) X-MSMail-Priority: Normal Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear CAFASPers, Kevin invites us all to Santa Cruz: Following the success of our first symposium on bioinformatics after CASP4, the University of California, Santa Cruz is hosting another one after CASP5 on Saturday and Sunday Dec 7-8, 2002. Full information can be found on the web at http://www.soe.ucsc.edu/research/compbio/workshop-2002.html Thank you, Kevin Karplus From casp5@bialko.llnl.gov Tue Aug 20 22:52:40 2002 Date: Tue, 20 Aug 2002 22:52:34 -0700 (PDT) From: CASP5 To: karplus@soe.ucsc.edu Subject: Last CASP5 target open for predictions /problems with early release of structural data X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear CASP predictor Target T0195 was the last target released in this Fifth round of CASP. We hope this will be a good prediction season for everyone participating! We inform with regret that due to an early release of pertinent structural information we have to withdraw target T0166 form CASP5. We also became aware of a similar release of information regarding target T0139. In cases like these, even if the problem becomes known after target's deadline, substantially lesser emphasis will be placed on that target's evaluation. However, the automatic evaluation performed at the Livermore Prediction Center will still be available. Final decisions regarding evaluation will be made by the CASP Organizing Committee and the CASP Independent Assessors. At the same time we would like to request that you inform us as soon as possible of any unduly released structural information of which you become aware. This will allow for prompt dissemination of such information to all predictors. Krzysztof Fidelis & Adam Zemla for CASP5 organizers From leszek@bioinfo.pl Wed Aug 21 03:17:22 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Livebench@Bioinfo. Pl" Subject: CAFASP -> CASP Date: Wed, 21 Aug 2002 12:17:50 +0200 Content-Type: text/plain; charset="ISO-8859-2" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear all, We have submitted until now targets T0129 - T0184 to CASP and we will send T0185 - T0187 today (black target names on http://bioinfo.pl/cafasp/3). It would be great if You could check (using Your server registration code) if we have not missed some models that should be sent to CASP (accepted CAFASP predictions). If there were no problems with Your servers before, all models should have been sent. In other cases irregularities are possible and I would rather send possibly missed models now than negotiate this after the CASP deadlines. Thanks a lot in advance. Yours, Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl From casp5@bialko.llnl.gov Tue Aug 20 19:19:03 2002 Date: Tue, 20 Aug 2002 19:18:57 -0700 (PDT) From: CASP5 To: karplus@soe.ucsc.edu Subject: Registration for CASP5 now open X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear CASP predictor or sympathizer The CASP5 meeting registration is now open. If you are interested in participating in the December 1-5, 2002, Asilomar meeting, please fill out the Participant Request Form as soon as possible. The last day to fill out this form will be September 15, 2002. Please note that due to limited space we cannot guarantee acceptance. Priority will be given to active predictors and those who register early. Meeting Participant Request Form is available at this address: http://predictioncenter.llnl.gov/casp5/meeting/registration.html The Asilomar Conference Canter is located in Pacific Grove, California. Krzysztof Fidelis for CASP5 organizers From casp5@bialko.llnl.gov Wed Aug 21 10:45:38 2002 Date: Wed, 21 Aug 2002 10:45:32 -0700 (PDT) From: CASP5 To: karplus@soe.ucsc.edu Subject: 2nd Biennial Symposium on Bioinformatics at UCSC X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Message from Kevin Karplus Following the success of the first symposium on bioinformatics after CASP4, the University of California, Santa Cruz is hosting another one after CASP5 on Saturday and Sunday Dec 7-8, 2002. Full information can be found on the web at http://www.soe.ucsc.edu/research/compbio/workshop-2002.html -- CASP5 Asilomar meeting is Dec. 1-5; The Symposium on Bioinformatics is Dec. 7-8. CASP organizers From casp5@bialko.llnl.gov Thu Aug 22 11:16:58 2002 Date: Thu, 22 Aug 2002 11:16:52 -0700 (PDT) From: CASP5 To: karplus@soe.ucsc.edu Subject: Target T0164 withdrawn from CASP5 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear CASP predictor Unfortunately there is one more target we have to withdraw from CASP due to early public release of structural information (T0164). Krzysztof Fidelis for CASP5 organizers From leszek@bioinfo.pl Fri Aug 23 09:12:33 2002 MIME-Version: 1.0 From: "Leszek Rychlewski" To: "Livebench@Bioinfo. Pl" Subject: CAFASP -> CASP Date: Fri, 23 Aug 2002 18:12:54 +0200 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear all, I asked You to check whether there are missing CAFASP models in the CASP repository but I got no complains back, so I had to check it myself :-). I have submitted few missing predictions (mainly protinfoab, cmap, hmmstr and some others). I hope I did not overwrite Your corrections, but this should not happened since if a model was corrected the original mail from us should not be accepted and should not overwrite the stored model. Anyway the http://bioinfo.pl/cafasp/3 page indicates now if the models where sent ("sent"). Looks like the Frost server did not register in CASP and we sent no models (please correct me or register if You want to be evaluated in CASP !!!). Good luck with the painful manual predictions :-) Yours, Leszek BioInfoBank Institute, Limanowskiego 24A/16, 60-744 Poznan, Poland Tel: +48-61-8653520, Fax: +48-61-8643350, E-mail: leszek@bioinfo.pl From karplus@bray.cse.ucsc.edu Thu Sep 5 00:36:09 2002 Date: Thu, 5 Sep 2002 00:36:05 -0700 From: Kevin Karplus To: adamz@llnl.gov, fidelis@llnl.gov CC: jmoult@tunc.org, th@samnger.ac.uk, karplus@soe.ucsc.edu Subject: T0169 I'm worried about my submission of target T0169. I submitted 5 models at about 20:23 tonight, well before the midnight deadline, but I never got any acknowledgement. I just checked, and they are not on the Prediction Center model list page. I'm going to resubmit them now, though it is past the deadline, under the assumption that they got lost in e-mail. I hope you will accept them. (If the first ones got stuck in your input queue and processed after I checked at 00:30, you may discard the newer submissions, as they are identical.) Kevin Karplus From karplus@bray.cse.ucsc.edu Thu Sep 5 06:35:18 2002 Date: Thu, 5 Sep 2002 06:35:15 -0700 From: Kevin Karplus To: adamx@llnl.gov, fidelis@llnl.gov CC: jmoult@tunc.org, th@sanger.ac.uk, Karplus@soe.ucsc.edu Subject: t0169 still not on list The resubmission I tried last night still hasn't resulted in any acknowledgements. I'm sending them again this morning, in the hope that whatever the problem was, it was temporary. Some of my e-mail is going out, as tested by a message I sent to myself through an e-mail alias on the other side of the country, so I don't see what else I can do at this end to get my models through. Kevin Kerplus From casp5@bialko.llnl.gov Thu Sep 5 14:24:36 2002 Date: Thu, 5 Sep 2002 14:24:30 -0700 (PDT) From: CASP5 To: karplus@soe.ucsc.edu Subject: Targets T0168-T0170 deadline extended X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear Predictors, >From yesterday 17PM till 11:30AM today we were experiencing a network problem at the lab. If you couldn't submit yesterday your models for targets T0168-T0170 please resubmit them now. The deadline for these targets has been extended till 5th of September midnight (24:00) local time in California (GMT - 7 hours). We are sorry for any inconveniences this may have caused you. For CASP5 organizers, Adam Zemla From kaf@grot.llnl.gov Tue Sep 10 20:20:14 2002 Date: Tue, 10 Sep 2002 20:20:09 -0700 (PDT) From: Krzysztof Fidelis To: karplus@cse.ucsc.edu Subject: CASP5 meeting registration reminder X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Dear CASP predictor or sympathizer This is a reminder that the last day to fill out the request form will be September 15, 2002. I would like to ask those requesting additional support to do so by Sept. 13th. Please note that due to limited space we cannot guarantee acceptance to the meeting. Priority will be given to active predictors and those who register early. Meeting Participant Request Form is available at this address: http://predictioncenter.llnl.gov/casp5/meeting/registration.html The Asilomar Conference Canter is located in Pacific Grove, California. Krzysztof Fidelis for CASP5 organizers From casp5@bialko.llnl.gov Wed Sep 11 16:07:34 2002 Date: Wed, 11 Sep 2002 16:07:28 -0700 (PDT) From: CASP5 To: karplus@soe.ucsc.edu Subject: First Student Addendum Conference to CASP X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Following suggestions raised at CASP4, an addendum meeting for students and post-docs will be held immediately following CASP at the Asilomar Conference Center, December 5-6, 2002. The meeting is expected to feature a large number of short, informal talks and time for focused discussion. Full information is not yet available, however, if you are interested in participating, please fill out the Participant Request Form as soon as possible. The last day to fill out this form will be September 25, 2002. Please note that due to limited space we cannot guarantee acceptance. Priority will be given to active predictors and those who register early. Meeting Participant Request Form is available at this address: http://predictioncenter.llnl.gov/casp5/meeting/registration2.htm Anyone willing to help organize the Student Addendum Conference, please send e-mail to parag@mbi.ucla.edu. -- CASP5 Asilomar meeting is Dec. 1-5; Student Addendum Conference is Dec. 5-6; The Symposium on Bioinformatics is Dec. 7-8. SAC-CASP organizers From kaf@grot.llnl.gov Fri Oct 11 19:06:36 2002 Date: Fri, 11 Oct 2002 19:06:30 -0700 (PDT) From: Krzysztof Fidelis To: karplus@soe.ucsc.edu Subject: CASP5 Registration X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear Predictor, We are pleased to inform you that your request to participate in CASP5, to be held December 1-5 at the Asilomar Conference Center in Pacific Grove, California, has been accepted. There is a waiting list for the meeting, so in order to maintain your place, please confirm your intention to attend by Oct. 18, 2002. Confirmations will be accepted by e-mail at: yadon1@llnl.gov Please specify the SUBJECT of your e-mail as: CONFIRMATION CASP5: YES/NO We are pleased to inform you that we are able to offer you a waiver of the registration fee and provide meals and single occupancy lodging at no charge. Krzysztof Fidelis, for CASP5 Organizers From rachelk@grunt.cse.ucsc.edu Wed Oct 16 18:40:25 2002 MIME-Version: 1.0 From: Rachel Karchin Content-Type: text/plain; charset=us-ascii Date: Wed, 16 Oct 2002 18:40:23 -0700 To: Krzysztof Fidelis CC: karplus@soe.ucsc.edu Subject: UCSC CASP5 team In-Reply-To: <5.1.0.14.2.20021016181744.03941b58@popcorn.llnl.gov> X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Hi Krzysztof: I'm not sure who registered for the meeting, but the UCSC team was: Kevin Karplus Richard Hughey Rachel Karchin Yael Mandel-Gutfreund Jenny Draper Jonathan Casper Oscar Hur I'm forwarding to Kevin, who can double-check that I didn't leave anyone out. -- rk Krzysztof Fidelis writes: > Rachel, > Could you send me names of all the members of your research group who > participated in CASP and registered for the meeting? (There seem to be more > than one from SC?). > Krzysztof > > > At 07:24 PM 10/11/2002 -0700, you wrote: > >Hi Krzysztof: > > > >I applied for financial support to attend the conference. > >to cover registration, lodging and meals. > > > >Who can I contact to find out whether I will be > >receiving the support? > > > >Thanks! > > > >Hope all is well over there (and not too hot) . . . > > > >-- rk > > > >--------------------------------------------------------------- > >Rachel Karchin > >bioinformatics Ph.D. candidate > >Office phone: (831) 459-5297 > >http://www.cse.ucsc.edu/~rachelk > >email: rachelk@cse.ucsc.edu > > > > > >Krzysztof Fidelis writes: > > > Dear Predictor, > > > > > > We are pleased to inform you that your request > > > to participate in CASP5, to be held December 1-5 > > > at the Asilomar Conference Center in Pacific > > > Grove, California, has been accepted. > > > > > > There is a waiting list for the meeting, so > > > in order to maintain your place, please confirm > > > your intention to attend by Oct. 18, 2002. > > > Confirmations will be accepted by e-mail at: > > > yadon1@llnl.gov > > > > > > Please specify the SUBJECT of your e-mail as: > > > CONFIRMATION CASP5: YES/NO > > > > > > Please send the meeting fees as soon as possible > > > but not later than Oct. 25, 2002. Details of > > > payment are specified at the following address: > > > > > > http://predictioncenter.llnl.gov/casp5/Casp5.html > > > > > > If you have any special difficulties with meeting > > > the above deadline please let us know > > > (yadon1@llnl.gov). > > > > > > The meeting fees are as follows: > > > > > > Registration fee: > > > Academics and members of not-for-profit > > > organizations $400 > > > Others $600 > > > > > > Lodging and Meals: > > > Double occupancy lodging $400 > > > Single occupancy lodging $630 > > > > > > Please send your payments in agreement with > > > the selections made during registration. > > > > > > Krzysztof Fidelis, > > > For CASP5 Organizers > > > > From karplus@bray.cse.ucsc.edu Thu Oct 17 09:33:34 2002 Date: Thu, 17 Oct 2002 09:33:29 -0700 From: Kevin Karplus To: fidelis@llnl.gov CC: rachelk@soe.ucsc.edu, karplus@soe.ucsc.edu In-reply-to: <15790.5383.887332.103669@grunt.cse.ucsc.edu> (message from Rachel Karchin on Wed, 16 Oct 2002 18:40:23 -0700) Subject: Re: UCSC CASP5 team Rachel's list Kevin Karplus Richard Hughey Rachel Karchin Yael Mandel-Gutfreund Jenny Draper Jonathan Casper Oscar Hur is correct for the faculty and for the students and postdocs actively involved in the the SAM-T02-human group. I would also add Mark Diekhans who, though not active in the predictions, did provide tools and tool support for building the template library. For the SAM-T02-server, the list is shorter Kevin Karplus Rachel Karchin Richard Hughey (one could also add former students who contributed to the tool building, but I don't think that is necessary) For the older SAM-T99-server, the list should be Kevin Karplus Spencer Tu Mark Diekhans Richard Hughey I have no research funding left, so any assistance that can be given for my students would be appreciated. Of the participants, besides me, Rachel is biggest contributor this year. Kevin Karplus From fidelis@llnl.gov Thu Oct 17 15:02:41 2002 MIME-Version: 1.0 X-Sender: e272374@popcorn.llnl.gov Date: Thu, 17 Oct 2002 14:59:24 -0700 To: Kevin Karplus From: Krzysztof Fidelis Subject: Re: UCSC CASP5 team In-Reply-To: <200210171633.g9HGXTl07742@bray.cse.ucsc.edu> Content-Type: text/plain; charset="us-ascii"; format=flowed X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Thanks Kevin, This is very helpful. I will let you know what I can do (less money this time here as well). Krzysztof At 09:33 AM 10/17/2002 -0700, you wrote: >Rachel's list > > Kevin Karplus > Richard Hughey > Rachel Karchin > Yael Mandel-Gutfreund > Jenny Draper > Jonathan Casper > Oscar Hur > >is correct for the faculty and for the students and postdocs actively >involved in the the SAM-T02-human group. > >I would also add > Mark Diekhans >who, though not active in the predictions, did provide tools and tool >support for building the template library. > >For the SAM-T02-server, the list is shorter > Kevin Karplus > Rachel Karchin > Richard Hughey >(one could also add former students who contributed to the tool >building, but I don't think that is necessary) > >For the older SAM-T99-server, the list should be > Kevin Karplus > Spencer Tu > Mark Diekhans > Richard Hughey > >I have no research funding left, so any assistance that can be given >for my students would be appreciated. Of the participants, besides >me, Rachel is biggest contributor this year. > >Kevin Karplus From dfischer@cs.bgu.ac.il Wed Oct 23 15:20:25 2002 MIME-Version: 1.0 X-Authentication-Warning: lace.cs.bgu.ac.il: dfischer owned process doing -bs Date: Thu, 24 Oct 2002 00:20:18 +0200 (IST) From: Daniel Fischer X-Sender: dfischer@lace To: karplus@soe.ucsc.edu Subject: casp, cafasp, post-casp Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Kevin, 1. I was thinking that your post-casp meeting would be an interesting opportunity to discuss a number of issues regarding cafasp, lb, eva, automated evaluation methods (such a painful topic...), plans for future experiments like pdb and mr-cafasp, etc. What do you think? Do you already have some preliminary schedule or list of speakers? 2. Regarding CAFASP results, we are in the process of evaluating the servers' performance (preliminary data show that samt02 performed very well, especially in the "easy HM targets" subset). We will soon ask feedback about our evaluations from some developers but won't make the results publicly available so we do not scoop CASP. Would you be willing to have a look at the results so we can get some feedback from you? D ------------------ Dr. Daniel Fischer Bioinformatics Dept. of Computer Science Ben Gurion University, Beer-Sheva 84015, Israel Tel +972-8-6472714 e-mail: dfischer@cs.bgu.ac.il Fax +972-8-6477650 or 6477648 http://www.cs.bgu.ac.il/~dfischer From karplus@bray.cse.ucsc.edu Wed Oct 23 17:02:28 2002 Date: Wed, 23 Oct 2002 17:02:21 -0700 From: Kevin Karplus To: dfischer@cs.bgu.ac.il CC: karplus@soe.ucsc.edu In-reply-to: (message from Daniel Fischer on Thu, 24 Oct 2002 00:20:18 +0200 (IST)) Subject: Re: casp, cafasp, post-casp I think there is still room for more speakers---contact katye@soe.ucsc.edu to get your name and the title of your talk on the list. I might be able to give you feedback on your evaluations, but I'm going to the Dagstuhl conference in November and I think I'll have to give 5 talks in 3 weeks then (1 Dagstuhl, 2 at Saarbruecken, 1 at CASP [assuming I did well enough], and one at a retirement event for my PhD advisor). I'm teaching this quarter as well, so with all my classes and grading, plus preparing 5 talks, I'm not sure I'll have any spare time before CASP. Kevin From katye@soe.ucsc.edu Fri Oct 25 14:15:52 2002 MIME-Version: 1.0 Date: Fri, 25 Oct 2002 14:15:52 -0700 From: Katy Elliott Organization: Center for Biomolecular Science & Engineering X-Accept-Language: en To: yadon1@llnl.gov CC: fidelis1@llnl.gov, karplus@soe.ucsc.edu Subject: IMPORTANT: Registration/Payment for Rachel Karchin Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Hello Denise- Per my voicemail to you-- We would like to confirm that Rachel Karchin is registered for CASP5, but because we are still determining how her registration will be paid (Krzysztof Fidelis is working on getting Rachel financial aid through the conference), and because the payment deadline is ostensibly today, we would like to request that she remain on the registration list until we can resolve her payment source. Thank you for any help or information you have on this matter. I look forward to hearing from you! Sincerely, Katy Elliott -- Katy Elliott Administrative Manager Center for Biomolecular Science & Engineering University of California, Santa Cruz 312B Baskin Engineering Voice: (831) 459-4366 Fax: (831) 459-4829 From katye@soe.ucsc.edu Fri Oct 25 16:13:30 2002 MIME-Version: 1.0 Date: Fri, 25 Oct 2002 16:13:29 -0700 From: Katy Elliott Organization: Center for Biomolecular Science & Engineering X-Accept-Language: en To: Kevin Karplus Subject: Re: CASP5 Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Kevin- I'll be sending an email on Rachel's behalf this afternoon (will cc you), and will get back to you with recommendation about which funding source we can use on Monday. Shouldn't be a problem to get our Business Office to cut a check next week. Katy Kevin Karplus wrote: > Rachel, Krystof agreed to waive registration fees, leaving us with $400 to > come up with. You should send e-mail (or reply to Krystof's > mail) saying you are definitely coming, and that the $400 will be > found and sent soon. > > Jenny, Krystof said that you had indicated an interest in the > conference, but had not replied by the deadline, so he was dropping > you from the list. > > Katy, if you can shake loose $400 from one of the accounts to cover > Rachel's housing at the conference, it would be appreciated. Rachel > should have the information about where to send the money. > > Thanks, > Kevin -- Katy Elliott Administrative Manager Center for Biomolecular Science & Engineering University of California, Santa Cruz 312B Baskin Engineering Voice: (831) 459-4366 Fax: (831) 459-4829 From katye@soe.ucsc.edu Fri Oct 25 16:27:29 2002 MIME-Version: 1.0 Date: Fri, 25 Oct 2002 16:27:27 -0700 From: Katy Elliott Organization: Center for Biomolecular Science & Engineering X-Accept-Language: en To: yadon1@llnl.gov CC: Rachel Karchin , Kevin Karplus Subject: IMPORTANT: Update on Rachel Karchin/CASP5 Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Ms. Yadon- This is to confirm that Rachel Karchin still plans to attend CASP 5, and per a phone conversation this afternoon between Kevin Karplus (our group leader) and Krzysztof Fidelis, Mr. Fidelis verified that Rachel has been awarded financial support. Her registration fees are slated to be paid by the conference. We will pay for her lodging, but the check cannot be cut and mailed until late next week. Can we prevail on you to reserve her a double occupancy hotel room in the meantime? Please do consider this email official confirmation that her $400 lodging fee will be paid. Thank you, and I look forward to hearing from you. Sincerely, Katy Elliott -- Katy Elliott Administrative Manager Center for Biomolecular Science & Engineering University of California, Santa Cruz 312B Baskin Engineering Voice: (831) 459-4366 Fax: (831) 459-4829 From learithe@croak.cse.ucsc.edu Fri Oct 25 16:30:07 2002 MIME-Version: 1.0 Date: Fri, 25 Oct 2002 16:30:45 -0700 (PDT) From: Jenny Draper To: Kevin Karplus cc: rachelk@soe.ucsc.edu, , Subject: Re: CASP5 In-Reply-To: <200210252200.g9PM00132744@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK I sent a reply on the day of the deadline 10/18/02, to request being dropped, as I can't afford the registration fee. Hopefully get got the message eventually? The message was sent to "yadon1@llnl.gov" ?! -Jenny Draper ======================================================================= On Fri, 25 Oct 2002, Kevin Karplus wrote: > > Rachel, Krystof agreed to waive registration fees, leaving us with $400 to > come up with. You should send e-mail (or reply to Krystof's > mail) saying you are definitely coming, and that the $400 will be > found and sent soon. > > Jenny, Krystof said that you had indicated an interest in the > conference, but had not replied by the deadline, so he was dropping > you from the list. > > Katy, if you can shake loose $400 from one of the accounts to cover > Rachel's housing at the conference, it would be appreciated. Rachel > should have the information about where to send the money. > > Thanks, > Kevin > > From rachelk@grunt.cse.ucsc.edu Mon Oct 28 07:59:37 2002 MIME-Version: 1.0 From: Rachel Karchin Content-Type: text/plain; charset=us-ascii Date: Mon, 28 Oct 2002 07:59:35 -0800 To: Krzysztof Fidelis Cc: karplus@soe.ucsc.edu, katye@soe.ucsc.edu, yadon1@llnl.gov, rachelk@soe.ucsc.edu Subject: CASP5 LATE PAYMENT for Rachel Karchin In-Reply-To: <200210280650.WAA121452@grot.llnl.gov> X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Hi Krzysztof: I'm hoping you sent me the message below in error. Per your conversation on Friday with Kevin Karplus, you agreed to waive the $400 conference fee for me. A $400 check for lodging fees will be forthcoming from UCSC's Center for Biomolecular Science and Engineering. We have called Ms. Yadon twice already to confirm the waiver and my conference registration status, but, to my knowledge, she has not returned our calls. I will be away from my office today, due to a family medical situation, so please contact (or have Denise or Lisa contact) Katy Elliot, CBSE administrative manager, to discuss the details of payment for the remaining $400. katye@soe.ucsc.edu 831-459-4366 -- rk ------------------------------------------------------- Rachel Karchin bioinformatics Ph.D. candidate Office phone: (831) 459-5297 http://www.cse.ucsc.edu/~rachelk email: rachelk@cse.ucsc.edu Krzysztof Fidelis writes: > > Dear Predictor: > > Our records show that we have not received your payment > by the October 25th deadline. There is a long waiting list > for the meeting, so we really must collect your payment > at this time. If we do not hear from you by Tuesday, > October 29th, we will offer your place to someone on > the waiting list. > > Please contact Ms. Denise Yadon at (925) 423 0920 to submit > your payment with a credit card. > > If you have already submitted your payment (either by credit > card or by mail postmarked by October 25th) but still received > this message, please contact Ms. Lisa Lopez at lopez68@llnl.gov. > Please specify the subject of your message as: > CASP5 PAYMENT SUBMITTED. > > In all other cases please contact me directly at > fidelis@llnl.gov. > > Krzysztof Fidelis > For CASP5 organizers > > > > > > From dfischer@cs.bgu.ac.il Mon Oct 28 10:49:46 2002 MIME-Version: 1.0 X-Authentication-Warning: silver.cs.bgu.ac.il: dfischer owned process doing -bs Date: Mon, 28 Oct 2002 20:48:57 +0200 (IST) From: Daniel Fischer X-Sender: dfischer@silver To: Kevin Karplus Subject: Re: casp, cafasp, post-casp In-Reply-To: <200210240002.g9O02Lh15983@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Kevin, I understand how busy this session is. I think we will have enough feedback from a few other developers. Thanks, D ------------------ Dr. Daniel Fischer Bioinformatics Dept. of Computer Science Ben Gurion University, Beer-Sheva 84015, Israel Tel +972-8-6472714 e-mail: dfischer@cs.bgu.ac.il Fax +972-8-6477650 or 6477648 http://www.cs.bgu.ac.il/~dfischer On Wed, 23 Oct 2002, Kevin Karplus wrote: > > I think there is still room for more speakers---contact > katye@soe.ucsc.edu to get your name and the title of your talk on the > list. > > > I might be able to give you feedback on your evaluations, but I'm > going to the Dagstuhl conference in November and I think I'll have to > give 5 talks in 3 weeks then (1 Dagstuhl, 2 at Saarbruecken, 1 at CASP > [assuming I did well enough], and one at a retirement event for my PhD > advisor).I'm teaching this quarter as well, so with all my classes > and grading, plus preparing 5 talks, I'm not sure I'll have any spare > time before CASP. > > Kevin > From tmw@grot.llnl.gov Wed Oct 23 20:50:33 2002 Date: Wed, 23 Oct 2002 20:50:27 -0700 (PDT) From: PredicitonCenter To: karplus@soe.ucsc.edu Subject: TMW:PREDICTING HIGH IMPACT PROTEIN STRUCTURES X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear CASP Predictor: The limited availability of crystallographic and NMR data puts many research projects in biology at a disadvantage. At the last CASP meeting it was suggested that as a structure prediction community, we might be able to remedy this situation, even if in a small part, for a few, diverse, biologically important target proteins. In the time between CASP5 prediction season and the meeting itself we would like to invite you to take part in the Ten Most Wanted, an experiment in modeling high impact protein structures, for which structural data is not likely to appear in the near future. Your participation, and that of other CASP-affiliated prediction groups worldwide, will assure the highest quality of models presently attainable. The targets were chosen, in part, because of the significant potential for impact the models generated by the structure prediction community will have on the science of each of the selected projects. We hope you will join in this community wide effort. Details of the Ten Most Wanted experiment, the targets themselves, and instructions for uploading predictions can be obtained from http://tmw.llnl.gov. We intend to discuss the results of the experiment at the CASP5 meeting. The deadline for submitting models in this round is November 15, 2002. David Baker Krzysztof Fidelis Mike Firpo Dani Fischer Dietlind Gerloff Barry Honig Andrei Lupas Parag Mallick Eugene Melamud John Moult Ram Samudrala Adam Zemla From karplus@bray.cse.ucsc.edu Tue Oct 29 15:41:05 2002 Date: Tue, 29 Oct 2002 15:41:02 -0800 From: Kevin Karplus To: tmw@grot.llnl.gov CC: karplus@soe.ucsc.edu In-reply-to: <200210240350.UAA115466@grot.llnl.gov> (message from PredicitonCenter on Wed, 23 Oct 2002 20:50:27 -0700 (PDT)) Subject: Re: TMW:PREDICTING HIGH IMPACT PROTEIN STRUCTURES I'm sorry, I won't be able to participate in the TMW prediction cycle this time around---I'm swamped with work and only just beginning to get caught up with everything that slipped because of CASP5 running past the scheduled end date. I'm only paying one grad student this year, and she has to finish up her PhD thesis. The volunteers that I might be able to get are too busy this quarter for the intense effort needed to provide any benefit past what an automatic server can do. I have no objection to the SAM-T02 server being used for the TMW predictions, of course, but I can't do much beyond what the server does in the time available. The deadlines are simply too tight for me to schedule my limited research time for this. Kevin Karplus From fidelis@llnl.gov Mon Oct 28 21:35:48 2002 MIME-Version: 1.0 X-Sender: e272374@popcorn.llnl.gov Date: Mon, 28 Oct 2002 20:36:08 -0800 To: CASP5_Predictors:; From: Krzysztof Fidelis Subject: CASP5 Abstracts Content-Type: multipart/mixed; boundary="=====================_1326626598==_" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --=====================_1326626598==_ Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CASP5 Predictor: It is now time for submission of CASP5 abstracts. This information is essential for two reasons, first it will be made available to the meeting participants, and second it will be used by the assessors to complete their work and to select speakers. We are now requesting submission of METHODS ABSTRACTS from all groups taking part in CASP5. Methods abstracts should provide a concise and clear description of the approach tested in CASP5. Please provide a reasonably complete account of your technique so the reader can grasp the most important points without referring to additional material. Methods abstracts will be accepted from all groups predicting at CASP5, regardless if they plan to attend the meeting itself. At this time we also invite submission of POSTER ABSTRACTS and SOFTWARE DEMONSTRATION ABSTRACTS. Poster size and the details of the available workstations will be announced shortly. Abstracts should be formatted according to the enclosed "abstract_requirements" and "abstract_template" files. Please send your abstracts AS ATTACHMENTS to Andriy Kryshtafovych at andriy@llnl.gov Please use the following SUBJECT lines: For methods abstracts: "CASP5-M-Group_Name", for poster abstracts: "CASP5-P-Group_Name" , for software demonstration abstracts: "CASP5-S-Group_Name" , where Group_Name should be substituted by your group name. The deadline for submitting abstracts is November 5, 2002. 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Please refer to other work as follows [1-2]. \par \par Throughout the text please use Times New Roman, 10pt. and single spacing. Please skip one line between paragraphs. No indentations. Please skip one line before reference block. Please refer to other work as follows [1-2]. \par \par Throughout the text please use Times New Roman, 10pt. and single spacing. Please skip one line between paragraphs. No indentations. Please skip one line before reference block. Please refer to other work as follows [1-2]. \par \par Throughout the text please use Times New Roman, 10pt. and single spacing. Please skip one line between paragraphs. No indentations. Please skip one line before reference block. Please refer to other work as follows [1-2]. \par \par Throughout the text please use Times New Roman, 10pt. and single spacing. Please skip one line between paragraphs. No indentations. Please skip one line before reference block. 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Please refer to other work as follows [1-2]. \par \par Throughout the text please use Times New Roman, 10pt. and single spacing. Please skip one line between paragraphs. No indentations. Please skip one line before reference block. Please refer to other work as follows [1-2]. \par \par Throughout the text please use Times New Roman, 10pt. and single spacing. Please skip one line between paragraphs. No indentations. Please skip one line before reference block. Please refer to other work as follows [1-2]. \par \par {\listtext\pard\plain\s18 \fs20\lang1036\langfe1033\langnp1036\insrsid5458970\charrsid13007493 \hich\af0\dbch\af0\loch\f0 1.\tab}}\pard\plain \s18\qj \fi-360\li360\ri0\widctlpar\jclisttab\tx360\aspalpha\aspnum\faauto\ls2\adjustright\rin0\lin360\itap0 \fs24\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {\fs20\lang1036\langfe1033\langnp1036\insrsid5458970\charrsid13007493 Altschul S.F. et al. }{\fs20\insrsid5458970 (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. }{\i\fs20\insrsid5458970 Nucleic Acids Res.}{\fs20\insrsid5458970 }{\b\i\fs20\insrsid5458970 25 }{\i\fs20\insrsid5458970 (17),}{\fs20\insrsid5458970 3389-3402 \par {\listtext\pard\plain\s18 \fs20\insrsid5458970 \hich\af0\dbch\af0\loch\f0 2.\tab}Jones D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices}{\i\fs20\insrsid5458970 . J. Mol. 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Use the following layout (no indentation from the left margin): \par }\pard\plain \s18\qj \li0\ri0\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \fs24\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {\insrsid5269067 \par {\listtext\pard\plain\s18 \lang1036\langfe1033\langnp1036\insrsid5269067\charrsid13372655 \hich\af0\dbch\af0\loch\f0 1.\tab}}\pard \s18\qj \fi-360\li360\ri0\widctlpar\jclisttab\tx360\aspalpha\aspnum\faauto\ls3\adjustright\rin0\lin360\itap0 { \lang1036\langfe1033\langnp1036\insrsid5269067\charrsid13372655 Altschul S.F. et al. }{\insrsid5269067 (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. }{\i\insrsid5269067 Nucleic Acids Res.}{\insrsid5269067 }{ \b\i\insrsid5269067 25 }{\i\insrsid5269067 (17),}{\insrsid5269067 3389-3402. \par }\pard \s18\qj \li0\ri0\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid5269067 {\insrsid5269067 \par }\pard \s18\qj \fi720\li0\ri0\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 {\insrsid5269067 \par }} --=====================_1326626598==_-- From fidelis@llnl.gov Tue Nov 5 00:18:12 2002 MIME-Version: 1.0 X-Sender: e272374@popcorn.llnl.gov Date: Mon, 04 Nov 2002 23:22:23 -0800 To: CASP5_Predictors:; From: Krzysztof Fidelis Subject: CASP5 ABSTRACT SUBMISSION DEADLINE Content-Type: multipart/mixed; boundary="=====================_117224690==_" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --=====================_117224690==_ Content-Type: multipart/alternative; boundary="=====================_117224690==_.ALT" --=====================_117224690==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CASP5 Predictors: We would like to thank all of you who have already submitted your abstracts. We would also like to remind those of you who have not done this yet that the deadline is TOMORROW, November 5, 2002, Midnight, PST. Due to the printing schedule we will not be able to include abstracts received past this deadline in the CASP5 Conference Book. Please strictly follow the abstract submission guidelines. Special notes regarding this matter: * No PDF files will be accepted. * Please send only one abstract per e-mail. * Please follow the template in all the details, including "STYLE", e.g. "heading", "body text", etc. I include the rest of the original message and the abstract template for easy reference: Methods abstracts should provide a concise and clear description of the approach tested in CASP5. Please provide a reasonably complete account of your technique so the reader may grasp the most important points without referring to additional material. Methods abstracts will be accepted from all groups predicting at CASP5, regardless if they plan to attend the meeting itself. At this time we also invite submission of POSTER ABSTRACTS and SOFTWARE DEMONSTRATION ABSTRACTS. Abstracts should be formatted according to the enclosed "abstract_requirements" and "abstract_template" files. Please send your abstracts AS ATTACHMENTS to Andriy Kryshtafovych at andriy@llnl.gov Please use the following SUBJECT lines: For methods abstracts: "CASP5-M-Group_Name", for poster abstracts: "CASP5-P-Group_Name" , for software demonstration abstracts: "CASP5-S-Group_Name" , where Group_Name should be substituted by your group name. The deadline for submitting abstracts is November 5, 2002. Krzysztof Fidelis for CASP5 organizers --=====================_117224690==_.ALT Content-Type: text/html; charset="us-ascii" Dear CASP5 Predictors:

We would like to thank all of you who have already submitted your abstracts. We would also like to remind those of you who have not done this yet that the deadline is TOMORROW, November 5, 2002, Midnight, PST. Due to the printing schedule we will not be able to include abstracts received past this deadline in the CASP5 Conference Book.

Please strictly follow the abstract submission guidelines. Special notes regarding this matter:
  • No PDF files will be accepted.
  • Please send only one abstract per e-mail.
  • Please follow the template in all the details, including “STYLE”, e.g. “heading”, “body text”, etc.
I include the rest of the original message and the abstract template for easy reference:

Methods abstracts should provide a concise and clear description of the approach tested in CASP5. Please provide a reasonably complete account of your technique so the reader may grasp the most important points without referring to additional material. Methods abstracts will be accepted from all groups predicting at CASP5, regardless if they plan to attend the meeting itself. 

At this time we also invite submission of POSTER ABSTRACTS and SOFTWARE DEMONSTRATION ABSTRACTS.

Abstracts should be formatted according to the enclosed “abstract_requirements” and  “abstract_template” files.

Please send your abstracts AS ATTACHMENTS to Andriy Kryshtafovych at
andriy@llnl.gov

Please use the following SUBJECT lines:

For methods abstracts: “CASP5-M-Group_Name”,
for poster abstracts: “CASP5-P-Group_Name” ,
for software demonstration abstracts: “CASP5-S-Group_Name” ,

where Group_Name should be substituted by your group name.

The deadline for submitting abstracts is November 5, 2002.

Krzysztof Fidelis
for CASP5 organizers






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Use the following layout (no indentation from the left margin): \par }\pard\plain \s18\qj \li0\ri0\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \fs24\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {\insrsid5269067 \par {\listtext\pard\plain\s18 \lang1036\langfe1033\langnp1036\insrsid5269067\charrsid13372655 \hich\af0\dbch\af0\loch\f0 1.\tab}}\pard \s18\qj \fi-360\li360\ri0\widctlpar\jclisttab\tx360\aspalpha\aspnum\faauto\ls3\adjustright\rin0\lin360\itap0 { \lang1036\langfe1033\langnp1036\insrsid5269067\charrsid13372655 Altschul S.F. et al. }{\insrsid5269067 (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. }{\i\insrsid5269067 Nucleic Acids Res.}{\insrsid5269067 }{ \b\i\insrsid5269067 25 }{\i\insrsid5269067 (17),}{\insrsid5269067 3389-3402. \par }\pard \s18\qj \li0\ri0\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid5269067 {\insrsid5269067 \par }\pard \s18\qj \fi720\li0\ri0\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 {\insrsid5269067 \par }} --=====================_117224690==_-- From karplus@bray.cse.ucsc.edu Tue Nov 5 09:38:14 2002 Date: Tue, 5 Nov 2002 09:38:08 -0800 From: Kevin Karplus To: fidelis@llnl.gov Cc: karplus@soe.ucsc.edu In-reply-to: <5.1.0.14.2.20021104231431.03123be0@popcorn.llnl.gov> (message from Krzysztof Fidelis on Mon, 04 Nov 2002 23:22:23 -0800) Subject: Re: CASP5 ABSTRACT SUBMISSION DEADLINE My mailer does not do attachments---can I send abstracts as plain text? From karplus@bray.cse.ucsc.edu Tue Nov 5 09:45:33 2002 Date: Tue, 5 Nov 2002 09:45:32 -0800 From: Kevin Karplus To: rachelk@soe.ucsc.edu CC: karplus@soe.ucsc.edu Subject: CASP5 abstract Did you submit the abstract for the SAM-T02 server to CASP5? The deadline is today. From karplus@bray.cse.ucsc.edu Tue Nov 5 09:52:15 2002 Date: Tue, 5 Nov 2002 09:52:09 -0800 From: Kevin Karplus To: fidelis@llnl.gov CC: karplus@soe.ucsc.edu In-reply-to: <5.1.0.14.2.20021028203327.03afe3e0@popcorn.llnl.gov> (message from Krzysztof Fidelis on Mon, 28 Oct 2002 20:36:08 -0800) Subject: Re: CASP5 Abstracts Further problem---I don't have any tools that use RTF format, and there is not time for me to learn how to use a whole suite of new word-processing tools today. I can't even read the RTF files you sent to explain the format. I'm going to have to send plain text files, since there is no way I can do RTF in the available time. From andriy@llnl.gov Tue Nov 5 10:14:25 2002 MIME-Version: 1.0 X-Sender: e004172@poptop.llnl.gov Date: Tue, 05 Nov 2002 10:10:49 -0800 To: Kevin Karplus From: Andriy Kryshtafovych Subject: Re: CASP5-M-SAM-T02-human In-Reply-To: <200211051800.gA5I0IO13919@bray.cse.ucsc.edu> Content-Type: multipart/alternative; boundary="=====================_325415723==_.ALT" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --=====================_325415723==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Kevin, Please ATTACH the abstract to your e-mail. Thanks, Andriy ************************************************ Dr. Andriy Kryshtafovych Computational & Systems Biology Biology & Biotechnology Research Program Lawrence Livermore National Laboratory 7000 East Ave. , P.O. Box 808, MS L-448 Livermore, CA 94550, USA e-mail: andriy@llnl.gov phone: (925) 424-5859 fax: (925) 424-3130 --=====================_325415723==_.ALT Content-Type: text/html; charset="us-ascii" Kevin,

Please ATTACH the abstract to your e-mail.

Thanks,
Andriy

************************************************
Dr. Andriy Kryshtafovych
Computational & Systems Biology
Biology & Biotechnology Research Program
Lawrence Livermore National Laboratory
7000 East Ave. , P.O. Box 808, MS L-448
Livermore, CA 94550, USA
e-mail: andriy@llnl.gov
phone: (925) 424-5859
fax:       (925) 424-3130
--=====================_325415723==_.ALT-- From karplus@bray.cse.ucsc.edu Tue Nov 5 10:17:59 2002 Date: Tue, 5 Nov 2002 10:17:58 -0800 From: Kevin Karplus To: andriy@llnl.gov CC: karplus@soe.ucsc.edu In-reply-to: <5.1.0.14.2.20021105100917.02beccf8@poptop.llnl.gov> (message from Andriy Kryshtafovych on Tue, 05 Nov 2002 10:10:49 -0800) Subject: Re: CASP5-M-SAM-T02-human I'm sorry, my mailer does not do attachments. I also don't know how to use any of the word processors that use RTF, so I sent in plain text. From fidelis@llnl.gov Tue Nov 5 13:24:14 2002 MIME-Version: 1.0 X-Sender: e272374@popcorn.llnl.gov Date: Tue, 05 Nov 2002 11:20:05 -0800 To: CASP5_Predictors:; From: Krzysztof Fidelis Subject: ABSTRACT TEMPLATE - NEW DEADLINE Content-Type: multipart/mixed; boundary="=====================_160284747==_" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --=====================_160284747==_ Content-Type: multipart/alternative; boundary="=====================_160284757==_.ALT" --=====================_160284757==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CASP5 Predictors: Yesterday I have mailed you a slightly different version of the abstract template relative to the original mailing. Some of you have noticed that. Please use any of the two versions. I include the original (and preferred) version with this e-mail. Due to this confusion we are extending the abstract collection deadline to Nov. 6, Noon, PST. Krzysztof Fidelis for CASP5 organizers Please follow the abstract submission guidelines strictly. Special notes regarding this matter: * No PDF files will be accepted. * Please send one abstract per e-mail. * Please follow the template in all the details, including "STYLE", e.g "heading", "body text", etc. * Please adhere to the SUBJECT line standards (see below) I include the rest of the original message and abstract template for easy reference: Methods abstracts should provide a concise and clear description of the approach tested in CASP5. Please provide a reasonably complete account of your technique so the reader may grasp the most important points without referring to additional material. Methods abstracts will be accepted from all groups predicting at CASP5, regardless if they plan to attend the meeting itself. At this time we also invite submission of POSTER ABSTRACTS and SOFTWARE DEMONSTRATION ABSTRACTS. Abstracts should be formatted according to the enclosed "abstract_requirements" and "abstract_template" files. Please send your abstracts AS ATTACHMENTS to Andriy Kryshtafovych at andriy@llnl.gov Please use the following SUBJECT lines: For methods abstracts: "CASP5-M-Group_Name", for poster abstracts: "CASP5-P-Group_Name" , for software demonstration abstracts: "CASP5-S-Group_Name" , where Group_Name should be substituted by your group name. --=====================_160284757==_.ALT Content-Type: text/html; charset="us-ascii" Dear CASP5 Predictors:

Yesterday I have mailed you a slightly different version of the abstract template relative to the original mailing. Some of you have noticed that. Please use any of the two versions. I include the original (and preferred) version with this e-mail. Due to this confusion we are extending the abstract collection deadline to Nov. 6, Noon, PST.

Krzysztof Fidelis
for CASP5 organizers

Please follow the abstract submission guidelines strictly. Special notes regarding this matter:

  • No PDF files will be accepted.
  • Please send one abstract per e-mail.
  • Please follow the template in all the details, including “STYLE”, e.g “heading”, “body text”, etc.
  • Please adhere to the SUBJECT line standards (see below)
I include the rest of the original message and abstract template for easy reference:

Methods abstracts should provide a concise and clear description of the approach tested in CASP5. Please provide a reasonably complete account of your technique so the reader may grasp the most important points without referring to additional material. Methods abstracts will be accepted from all groups predicting at CASP5, regardless if they plan to attend the meeting itself. 

At this time we also invite submission of POSTER ABSTRACTS and SOFTWARE DEMONSTRATION ABSTRACTS.

Abstracts should be formatted according to the enclosed “abstract_requirements” and  “abstract_template” files.

Please send your abstracts AS ATTACHMENTS to Andriy Kryshtafovych at
andriy@llnl.gov

Please use the following SUBJECT lines:

For methods abstracts: “CASP5-M-Group_Name”,
for poster abstracts: “CASP5-P-Group_Name” ,
for software demonstration abstracts: “CASP5-S-Group_Name” ,

where Group_Name should be substituted by your group name.



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Please refer to other work as follows [1-2]. \par \par Throughout the text please use Times New Roman, 10pt. and single spacing. Please skip one line between paragraphs. No indentations. Please skip one line before reference block. Please refer to other work as follows [1-2]. \par \par Throughout the text please use Times New Roman, 10pt. and single spacing. Please skip one line between paragraphs. No indentations. Please skip one line before reference block. Please refer to other work as follows [1-2]. \par \par Throughout the text please use Times New Roman, 10pt. and single spacing. Please skip one line between paragraphs. No indentations. Please skip one line before reference block. Please refer to other work as follows [1-2]. \par \par Throughout the text please use Times New Roman, 10pt. and single spacing. Please skip one line between paragraphs. No indentations. Please skip one line before reference block. Please refer to other work as follows [1-2]. \par \par Throughout the text please use Times New Roman, 10pt. and single spacing. Please skip one line between paragraphs. No indentations. Please skip one line before reference block. Please refer to other work as follows [1-2]. \par \par Throughout the text please use Times New Roman, 10pt. and single spacing. Please skip one line between paragraphs. No indentations. Please skip one line before reference block. Please refer to other work as follows [1-2]. \par \par Throughout the text please use Times New Roman, 10pt. and single spacing. Please skip one line between paragraphs. No indentations. Please skip one line before reference block. Please refer to other work as follows [1-2]. \par \par Throughout the text please use Times New Roman, 10pt. and single spacing. Please skip one line between paragraphs. No indentations. Please skip one line before reference block. Please refer to other work as follows [1-2]. \par \par Throughout the text please use Times New Roman, 10pt. and single spacing. Please skip one line between paragraphs. No indentations. Please skip one line before reference block. Please refer to other work as follows [1-2]. \par \par Throughout the text please use Times New Roman, 10pt. and single spacing. Please skip one line between paragraphs. No indentations. Please skip one line before reference block. Please refer to other work as follows [1-2]. \par \par {\listtext\pard\plain\s18 \fs20\lang1036\langfe1033\langnp1036\insrsid5458970\charrsid13007493 \hich\af0\dbch\af0\loch\f0 1.\tab}}\pard\plain \s18\qj \fi-360\li360\ri0\widctlpar\jclisttab\tx360\aspalpha\aspnum\faauto\ls2\adjustright\rin0\lin360\itap0 \fs24\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {\fs20\lang1036\langfe1033\langnp1036\insrsid5458970\charrsid13007493 Altschul S.F. et al. }{\fs20\insrsid5458970 (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. }{\i\fs20\insrsid5458970 Nucleic Acids Res.}{\fs20\insrsid5458970 }{\b\i\fs20\insrsid5458970 25 }{\i\fs20\insrsid5458970 (17),}{\fs20\insrsid5458970 3389-3402 \par {\listtext\pard\plain\s18 \fs20\insrsid5458970 \hich\af0\dbch\af0\loch\f0 2.\tab}Jones D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices}{\i\fs20\insrsid5458970 . J. Mol. Biol.}{\b\i\fs20\insrsid5458970 292 }{ \i\fs20\insrsid5458970 (2)}{\fs20\insrsid5458970 , 195-202. \par }\pard \s18\qj \li720\ri0\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin720\itap0 {\fs20\insrsid5458970 \par \par \par }} --=====================_160284747==_-- From fidelis@llnl.gov Tue Nov 5 12:09:00 2002 MIME-Version: 1.0 X-Sender: e272374@popcorn.llnl.gov Date: Tue, 05 Nov 2002 12:05:23 -0800 To: Kevin Karplus From: Krzysztof Fidelis Subject: Re: CASP5 Abstracts In-Reply-To: <200211051752.gA5Hq9913604@bray.cse.ucsc.edu> Content-Type: multipart/alternative; boundary="=====================_163001744==_.ALT" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --=====================_163001744==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Kevin, I hope you can solve this problem - we will be waiting until tomorrow for your formatted version.Maybe Rachel could help? If we do not hear from you (correctly formatted abstract) - we will edit the abstract for you. Krzysztof At 09:52 AM 11/5/2002 -0800, you wrote: >Further problem---I don't have any tools that use RTF format, and >there is not time for me to learn how to use a whole suite of new >word-processing tools today. I can't even read the RTF files you sent >to explain the format. > >I'm going to have to send plain text files, since there is no way I >can do RTF in the available time. --=====================_163001744==_.ALT Content-Type: text/html; charset="us-ascii" Kevin,
I hope you can solve this problem - we will be waiting until tomorrow for your formatted version.Maybe Rachel could help? If we do not hear from you (correctly formatted abstract) - we will edit the abstract for you.
Krzysztof



At 09:52 AM 11/5/2002 -0800, you wrote:

Further problem---I don't have any tools that use RTF format, and
there is not time for me to learn how to use a whole suite of new
word-processing tools today.  I can't even read the RTF files you sent
to explain the format.

I'm going to have to send plain text files, since there is no way I
can do RTF in the available time.
--=====================_163001744==_.ALT-- From fidelis@llnl.gov Wed Nov 6 15:32:49 2002 MIME-Version: 1.0 X-Sender: e272374@popcorn.llnl.gov Date: Wed, 06 Nov 2002 14:31:33 -0800 To: CASP5_Predictors:; From: Krzysztof Fidelis Subject: Some questions for predictors Content-Type: multipart/alternative; boundary="=====================_258168356==_.ALT" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --=====================_258168356==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed To CASP5 Prediction Group Leaders, Please send us your answers to the multiple-choice questionnaire at the bottom of this letter. In order to expedite our processing of hundreds of these questionnaires, please format your answers in a simple string of the form: "PRED_QUEST_1111_2222_3333_01a02b03a04b05a06b07a08b09a10b11a12b13a14b". This format is an 11 character precursor followed by your 12 digit group leader code, and a series of 14 three-character-sets. There are 14 sets corresponding to the 14 questions in the questionnaire. Each three-character-set has two digits (denoting the number of the question) and a lowercase letter (denoting the answer to the respective question). The 11 character precursor is simply the quoted string: "PRED_QUEST_" (9 capital letters and 2 underscores). Please send your answers to the following email address: cm@predictioncenter.llnl.gov. Please put your group name and 12 digit predictor code in the subject of the letter, and the answer string in the body of the letter. Thank you, CASP5 Organizers P.S. If you have questions or comments about this process, please direct them to firpo2@llnl.gov. --------------------------------------------------- Questions for sequence based predictions: 1. Did you use multiple templates for: a. all targets you predicted b. none of the targets you predicted c. some of the targets you predicted 2. Did you use any available experimental information to improve your prediction? a. yes b. no 3. Did you treat the biologically important regions differently than the rest of the structure? a. yes, every time it was possible b. no c. sometimes 4. Did you use any method developed by your group and not available to others? a. yes b. no 5. If you answered yes to the previous question, was the in-house method used for a. template identification b. alignment c. loop prediction d. side chain prediction e. a combination of the above f. other 6. Did you manually refine the alignment for a. all targets you predicted b. none of the targets you predicted c. some of the targets you predicted 7. Did you use energy based refinement for a. all targets you predicted b. none of the targets you predicted c. some of the targets you predicted 8. Did you use a completely automatic program for a. all targets you predicted b. none of the targets you predicted c. some of the targets you predicted 9. Did you use a method not yet available in CASP4? a. yes b. no c. for some of the targets 10. If you answered yes to question 5, was the new method aimed at a. template identification b. alignment c. loop prediction d. side chain prediction e. other 11. Did you use known structure fragments for your loop prediction? a. yes b. no c. for some of the targets 12. Did you use a rotamer library for predicting the side chain conformation? a. yes b. no c. for some of the targets 13. Did you use any method to validate / rank your models? a. yes b. no c. for some of the targets 14. Did you make use of automatic model building servers at any stage of the prediction? a. yes b. no c. for some of the targets --=====================_258168356==_.ALT Content-Type: text/html; charset="us-ascii" To CASP5 Prediction Group Leaders,
Please send us your answers to the multiple-choice questionnaire at the bottom of this letter.
In order to expedite our processing of hundreds of these questionnaires, please format your answers in a simple string of the form: "PRED_QUEST_1111_2222_3333_01a02b03a04b05a06b07a08b09a10b11a12b13a14b". This format is an 11 character precursor followed by your 12 digit group leader code, and a series of 14 three-character-sets. There are 14 sets corresponding to the 14 questions in the questionnaire. Each three-character-set has two digits (denoting the number of the question) and a lowercase letter (denoting the answer to the respective question). The 11 character precursor is simply the quoted string: "PRED_QUEST_" (9 capital letters and 2 underscores).

Please send your answers to the following email address: cm@predictioncenter.llnl.gov. Please put your group name and 12 digit predictor code in the subject of the letter, and the answer string in the body of the letter.
Thank you,

CASP5 Organizers
P.S. If you have questions or comments about this process, please direct them to firpo2@llnl.gov.
---------------------------------------------------
Questions for sequence based predictions:

1. Did you use multiple templates for:
a. all targets you predicted
b. none of the targets you predicted
c. some of the targets you predicted


2. Did you use any available experimental information to improve your prediction?
a. yes
b. no


3. Did you treat the biologically important regions differently than the rest of the structure?
a. yes, every time it was possible
b. no
c. sometimes

4. Did you use any method developed by your group and not available to others?
a. yes
b. no


5. If you answered yes to the previous question, was the in-house method used for
a. template identification
b. alignment
c. loop prediction
d. side chain prediction
e. a combination of the above
f. other


6. Did you manually refine the alignment for
a. all targets you predicted
b. none of the targets you predicted
c. some of the targets you predicted


7. Did you use energy based refinement for
a. all targets you predicted
b. none of the targets you predicted
c. some of the targets you predicted


8. Did you use a completely automatic program for
a. all targets you predicted
b. none of the targets you predicted
c. some of the targets you predicted


9. Did you use a method not yet available in CASP4?
a. yes
b. no
c. for some of the targets


10. If you answered yes to question 5, was the new method aimed at
a. template identification
b. alignment
c. loop prediction
d. side chain prediction
e. other


11. Did you use known structure fragments for your loop prediction?
a. yes
b. no
c. for some of the targets


12. Did you use a rotamer library for predicting the side chain conformation?
a. yes
b. no
c. for some of the targets


13. Did you use any method to validate / rank your models?
a. yes
b. no
c. for some of the targets


14. Did you make use of automatic model building servers at any stage of the prediction?
a. yes

b. no
c. for some of the targets

--=====================_258168356==_.ALT-- From karplus@bray.cse.ucsc.edu Wed Nov 6 17:46:50 2002 Date: Wed, 6 Nov 2002 17:46:47 -0800 From: Kevin Karplus To: karplus@soe.ucsc.edu In-reply-to: <5.1.0.14.2.20021106142802.03209eb8@popcorn.llnl.gov> (message from Krzysztof Fidelis on Wed, 06 Nov 2002 14:31:33 -0800) Subject: Re: Some questions for predictors Copy of mail to cm@predictioncenter.llnl.gov CC: fidelis@llnl.gov, firpo2@llnl.gov Gack, what an awful format! Also some of the questions are unanswerable as phrased---the answers for those questions are just best guesses based on what I think you meant to ask. For example, Q1: "did you use multiple templates..." could be asking whether you used multiple templates to generate a single model, or whether multiple models were generated, each from a different template. I assumed the former interpretation, but someone else might very well put a different interpretation on the question. Another example: Q2 "did you use any available experimental information?" On some targets there was experimental information that we couldn't use. On others there was experimental information that we tried to use. On still others we didn't have enough time to look to see if there was experimental information. Is that a "yes" or a "no"? Another example: Q13 We didn't have any method for validating our models, but we did rank them (how else would we choose them)? Is this a "yes" or a "no"? Another example: for an automatic server entry and question 14. I'm assuming you want to know whether it used some OTHER automatic server. Also, it isn't clear whether using an ALIGNMENT server or a SECONDARY STRUCTURE server counts for hand predictors. Our method does not have "loop prediction" as a separate step from the rest of the algorithm, so the questions about "loop prediction" are particularly hard to interpret. Several of the questions, particularly 5 and 10, require multiple answers. As a result of multiple possible interpretations of the questions, I suspect that the results of this survey will be nearly meaningless. PRED_QUEST_4069_6308_1312_01a02b03c04a05abcdef06c07a08b09a10abcde11a12a13a14c PRED_QUEST_5035_2079_5263_01b02b03b04b0506b07b08a09a10abe11b12b13a14b PRED_QUEST_6269_7633_6117_01b02b03b04b0506b07b08a09b1011b12b13a14b PRED_QUEST_1549_8716_6404_01b02b03b04b0506b07b08a09a10e11b12b13a14b From firpo2@llnl.gov Tue Nov 12 17:02:58 2002 MIME-Version: 1.0 X-Sender: e276336@poptart.llnl.gov Date: Tue, 12 Nov 2002 16:57:29 -0800 To: CASP5 Predictors:; From: Mike Firpo Subject: Ten Most Wanted (TMW) Content-Type: text/plain; charset="us-ascii" ; format="flowed" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear CASP5 Predictor, Thank you for your participation in CASP5. We would encourage you also to take part in the Ten Most Wanted (TMW) experiment. All predictions submitted by Nov. 15 (this Friday) will be evaluated for preliminary results to be discussed at the CASP5 meeting in December. Thank you, CASP5 Organizers From firpo2@llnl.gov Tue Nov 12 17:07:12 2002 MIME-Version: 1.0 X-Sender: e276336@poptart.llnl.gov Date: Tue, 12 Nov 2002 17:07:36 -0800 To: karplus@soe.ucsc.edu From: Mike Firpo Subject: Ten Most Wanted (TMW) Content-Type: text/plain; charset="us-ascii" ; format="flowed" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear Kevin Karplus, We very much appreciate your contribution to CASP5 and would like to encourage you to submit predictions to the Ten Most Wanted (TMW) experiment. The predictions submitted by Nov. 15 (this Friday) will be evaluated for preliminary results to be discussed at the CASP5 meeting in December, where we will also discuss the future of this experiment. CASP5 Organizers From karplus@bray.cse.ucsc.edu Tue Nov 12 17:31:16 2002 Date: Tue, 12 Nov 2002 17:31:13 -0800 From: Kevin Karplus To: firpo2@llnl.gov CC: karplus@soe.ucsc.edu In-reply-to: (message from Mike Firpo on Tue, 12 Nov 2002 17:07:36 -0800) Subject: Re: Ten Most Wanted (TMW) Sorry, I can't do the TMW for this round---I'm going to the Dagstuhl conference next week, and I have 4 talks to prepare for the next 3 weeks before I go on Saturday (5 if I'm giving one at CASP). I also have a huge pile of homework to grade and another homework assignment to write. You are, of course, most welcome to run TMW targets through the SAM-T02 web server, but I don't have time to do any more than that. If there is another round, I'll probably have more time to participate, but I still haven't recovered from CASP5 running over by two weeks, which eliminated any preparation time before the beginning of Fall quarter. I like the idea of TMW, and hope I can participate in future. Kevin Karplus From firpo2@llnl.gov Wed Nov 13 09:43:18 2002 MIME-Version: 1.0 X-Sender: e276336@poptart.llnl.gov In-Reply-To: <200211130131.gAD1VD424398@bray.cse.ucsc.edu> Date: Wed, 13 Nov 2002 09:43:43 -0800 To: Kevin Karplus From: Mike Firpo Subject: Re: Ten Most Wanted (TMW) Content-Type: text/plain; charset="us-ascii" ; format="flowed" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Kevin, Thank you for your response. Good luck with your busy schedule. I'll look into running your server. We are looking forward to seeing you next month in Asilomar. Mike Firpo Prediction Center LLNL >Sorry, I can't do the TMW for this round---I'm going to the Dagstuhl >conference next week, and I have 4 talks to prepare for the next 3 >weeks before I go on Saturday (5 if I'm giving one at CASP). I also >have a huge pile of homework to grade and another homework assignment >to write. > >You are, of course, most welcome to run TMW targets through the >SAM-T02 web server, but I don't have time to do any more than that. > >If there is another round, I'll probably have more time to >participate, but I still haven't recovered from CASP5 running over by >two weeks, which eliminated any preparation time before the beginning >of Fall quarter. > >I like the idea of TMW, and hope I can participate in future. > >Kevin Karplus From firpo2@llnl.gov Wed Nov 13 10:16:46 2002 MIME-Version: 1.0 X-Sender: e276336@poptart.llnl.gov In-Reply-To: <200211070146.gA71k7j30602@bray.cse.ucsc.edu> Date: Wed, 13 Nov 2002 10:17:12 -0800 To: Kevin Karplus From: Mike Firpo Subject: Re: Some questions for predictors Content-Type: text/plain; charset="us-ascii" ; format="flowed" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Kevin, I'm sorry for the delay in responding to this letter. I understand you have a heavy workload, so if you don't respond to this, i'll know why. The questionnaire is rather sloppy, and i'm sorry about that. Below are responses from the assessor to the specific questions you asked. If this helps, you can resend your answers. Cheers, Mike -------------------- > Q1: "did you use multiple templates..." could be asking > whether you used multiple templates to generate a single model, or > whether multiple models were generated, each from a different template. > I assumed the former interpretation, but someone else might very well > put a different interpretation on the question. > I meant using multiple template to build model 1. > Another example: Q2 "did you use any available experimental information?" > On some targets there was experimental information that we couldn't use. > On others there was experimental information that we tried to use. > On still others we didn't have enough time to look to see if there was > experimental information. Is that a "yes" or a "no"? > If on some of the models experimental information was used the answer is yes, if no attempt was made to use it on any model the answer should be no > Another example: Q13 We didn't have any method for validating our > models, but we did rank them (how else would we choose them)? Is this > a "yes" or a "no"? > The answer should be yes in this case. You could just build one and not need to use any ranking (especially for pure CM targets) > Another example: for an automatic server entry and question 14. I'm > assuming you want to know whether it used some OTHER automatic server. > Also, it isn't clear whether using an ALIGNMENT server or a SECONDARY > STRUCTURE server counts for hand predictors. This question is not meant to be answered by servers (sorry didn't think of that). The meaning of the question was to assess whether people used results from MODEL BUILDING (that is servers that return coordinates) servers to get an initial model > > Our method does not have "loop prediction" as a separate step from the > rest of the algorithm, so the questions about "loop prediction" are > particularly hard to interpret. It should still be possible to know whether the algorithm relies on fragments or not. From karplus@bray.cse.ucsc.edu Tue Nov 19 22:58:07 2002 Date: Tue, 19 Nov 2002 22:58:04 -0800 From: Kevin Karplus To: adamz@llnl.gov, fidelis@llnl.gov, jmoult@tunc.org, th@samnger.ac.uk Cc: karplus@soe.ucsc.edu Subject: CASP5 talk? I'm curious when the CASP5 speakers will be informed that they need to prepare a talk (or if they have been already). The conference is only 10 days away, and I haven't heard anything yet about whether I need to prepare a talk. I am, of course, hoping to be invited, but I have no idea which targets I did well or poorly on. The predictors were not given an early look at the correct structures this year, so I couldn't even begin to guess. Kevin Karplus From jmoult@tunc.org Wed Nov 20 04:17:16 2002 MIME-Version: 1.0 Date: Wed, 20 Nov 2002 07:16:49 -0500 From: John Moult Subject: Re: CASP5 talk? In-reply-to: <200211200658.gAK6w4N23074@bray.cse.ucsc.edu> X-Sender: moult@comcast.net To: Kevin Karplus , adamz@llnl.gov, fidelis@llnl.gov, th@sanger.ac.uk Content-type: text/plain; charset=us-ascii; format=flowed X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Kevin: At 10:58 PM 11/19/2002 -0800, Kevin Karplus wrote: >I'm curious when the CASP5 speakers will be informed that they need to >prepare a talk (or if they have been already). So am I... >The conference is only >10 days away, and I haven't heard anything yet about whether I need to >prepare a talk. By CASP standards, bags of time to get things finished. >I am, of course, hoping to be invited, but I have no idea which >targets I did well or poorly on. The predictors were not given an >early look at the correct structures this year, so I couldn't even >begin to guess. According to records, we are also on track here. Well, may be I should not be facetious Kevin. However, this sort of message really does not tell the organizers any thing they do not know really rather well already. I think it is correct that we are about on schedule compared with other CASPs. To which you will no doubt respond 'but you have always been too late'. Can't argue with that. Also can't do it any earlier, in spite of considerable effort. John. From karplus@bray.cse.ucsc.edu Wed Nov 20 05:08:39 2002 Date: Wed, 20 Nov 2002 05:08:35 -0800 From: Kevin Karplus To: jmoult@tunc.org CC: adamz@llnl.gov, fidelis@llnl.gov, th@sanger.ac.uk, karplus@soe.ucsc.edu In-reply-to: <5.1.0.14.2.20021120071102.03148eb0@pop.earthlink.net> (message from John Moult on Wed, 20 Nov 2002 07:16:49 -0500) Subject: Re: CASP5 talk? OK, I was mainly interested in knowing whether or not decisions had been made. I remember being very rushed in previous years, but have a vague recollection of having 2 weeks notice, so was beginning to worry that I might have missed a message. I'm reassured to know that no dcision has yet been made (the alternatives were worse). Thanks, Kevin Karplus From fidelis@llnl.gov Thu Nov 21 01:19:53 2002 MIME-Version: 1.0 X-Sender: e272374@popcorn.llnl.gov Date: Thu, 21 Nov 2002 00:24:07 -0800 To: CASP5_Predictors:; From: Krzysztof Fidelis Subject: TMW Sharing Page Content-Type: multipart/alternative; boundary="=====================_122045992==_.ALT" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --=====================_122045992==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CASP/TMW Predictors, In preparation for a discussion of the TMW experiment at CASP5 we have put together a Prediction Sharing Page. This page should be easy for browsing and downloading of predictions already made. To date there are approximately 200 models submitted to TMW. If you have any difficulty in using this page please let us know at firpo2@llnl.gov. Krzysztof Fidelis for CASP5/TMW organizers --=====================_122045992==_.ALT Content-Type: text/html; charset="us-ascii" Dear CASP/TMW Predictors,

In preparation for a discussion of the TMW experiment at CASP5 we have put together a Prediction Sharing Page. This page should be easy for browsing and downloading of predictions already made. To date there are approximately 200 models submitted to TMW. If you have any difficulty in using this page please let us know at firpo2@llnl.gov.

Krzysztof Fidelis
for CASP5/TMW organizers
--=====================_122045992==_.ALT-- From fidelis@llnl.gov Thu Nov 21 01:25:53 2002 MIME-Version: 1.0 X-Sender: e272374@popcorn.llnl.gov Date: Thu, 21 Nov 2002 00:37:45 -0800 To: CASP5_Predictors:; From: Krzysztof Fidelis Subject: CASP5 Software Demonstrations - Message from Eugene Melamud in charge of Software Demonstrations Content-Type: multipart/alternative; boundary="=====================_122864039==_.ALT" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --=====================_122864039==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CASP Predictors, The people from HP and SGI have kindly provided us with some computers for demos during CASP conference. We expect to get 3 octanes from SGI and 6 intel desktops from HP. The computers will be available for your use starting December 2nd in Marrill Hall. (Receptions and posters will be there too). Most people in the community use Linux for their computing needs so we are planning to convert four of the HP workstations to run Redhat. We are also planning to have an internet hookup, but available bandwidth will be severely limited. The only unlink from conference grounds is PcBell ISDN line, so if you have large files or programs, it might be a good idea to make a local copy and bring it with you. There should be plenty of a computational power on site and we encourage you make use of it for presentations. Please let me know if you want to reserve a time for your demo. For those of you with laptops, we are also planning to have a wireless access point in the Maryl Hall, so you guys can check email. If you have any specific requests or need a more detailed information about equipment, please send me an email at melamud@carb.nist.gov Eugene Melamud. --=====================_122864039==_.ALT Content-Type: text/html; charset="us-ascii" Dear CASP Predictors,

The people from HP and SGI have kindly provided us with some computers
for demos during CASP conference. We expect to get 3 octanes from SGI and
6 intel desktops from HP. The computers will be available for your use
starting December 2nd in Marrill Hall. (Receptions and posters will be there too).
Most people in the community use Linux for their computing needs so we
are planning to convert four of the HP workstations to run Redhat. We
are also planning to have an internet hookup, but available bandwidth
will be severely limited. The only unlink from conference grounds
is PcBell ISDN line, so if you have large files or programs, it might
be a good idea to make a local copy and bring it with you.
There should be plenty of a computational power on site and we
encourage you make use of it for presentations. Please let me know if
you want to reserve a time for your demo.

For those of you with laptops, we are also planning to have a
wireless access point in the Maryl Hall, so you guys can check email. If you
have any specific requests or need a more detailed information about
equipment, please send me an email at melamud@carb.nist.gov

Eugene Melamud.


--=====================_122864039==_.ALT-- From fidelis@llnl.gov Thu Nov 21 01:39:11 2002 MIME-Version: 1.0 X-Sender: e272374@popcorn.llnl.gov Date: Thu, 21 Nov 2002 00:46:28 -0800 To: CASP5_Predictors:; From: Krzysztof Fidelis Subject: CASP5 Poster Presentations Content-Type: multipart/alternative; boundary="=====================_123387391==_.ALT" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --=====================_123387391==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed The normal CASP5 poster board allocation will be a 4'x4' area (feet). If for any reason you would like to present a larger poster (4'x8') - please let me know as soon as possible, we may be able to accommodate you. Krzysztof Fidelis for CASP5 organizers --=====================_123387391==_.ALT Content-Type: text/html; charset="us-ascii" The normal CASP5 poster board allocation will be a 4'x4' area (feet). If for any reason you would like to present a larger poster (4'x8') - please let me know as soon as possible, we may be able to accommodate you.

Krzysztof Fidelis
for CASP5 organizers

--=====================_123387391==_.ALT-- From fidelis@llnl.gov Thu Nov 21 18:49:38 2002 MIME-Version: 1.0 X-Sender: e272374@popcorn.llnl.gov Date: Thu, 21 Nov 2002 17:54:04 -0800 To: CASP5_Predictors:; From: Krzysztof Fidelis Subject: CASP5 Speakers and Program, a message from John Moult Content-Type: multipart/alternative; boundary="=====================_185040714==_.ALT" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --=====================_185040714==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Predictors: Many of you are of course wondering whether speakers have yet been chosen for the Asilomar meeting. As usual with CASP, there has been an enormous amount of work to do before that could happen. However, the invitations have just starting to go out. I expect them all to have been sent by the end of Friday. The detailed program will not be available until shortly before the meeting. In outline: There will be an introduction to the CASP experiment on Sunday evening. Comparative modeling and fold recognition will be partly merged, and will be on Monday and Tuesday. New fold methods will be on Wednesday. On Thursday morning there will sessions on CAPRI, disorder prediction, and the Ten Most Wanted. See you there. John Moult for CASP Organizers and Assessors --=====================_185040714==_.ALT Content-Type: text/html; charset="us-ascii" Dear Predictors:

Many of you are of course wondering whether speakers have yet been chosen for the Asilomar meeting. As usual with CASP, there has been an enormous amount of work to do before that could happen. However, the invitations have just starting to go out. I expect them all to have been sent by the end of Friday.

The detailed program will not be available until shortly before the meeting. In outline: There will be an introduction to the CASP experiment on Sunday evening. Comparative modeling and fold recognition will be partly merged, and will be on Monday and Tuesday. New fold methods will be on Wednesday. On Thursday morning there will sessions on CAPRI, disorder prediction, and the Ten Most Wanted.

See you there.
John Moult
for CASP Organizers and Assessors



--=====================_185040714==_.ALT-- From fidelis@llnl.gov Sat Nov 23 12:02:11 2002 MIME-Version: 1.0 X-Sender: e272374@popcorn.llnl.gov Date: Sat, 23 Nov 2002 11:09:17 -0800 To: CASP5_Predictors:; From: Krzysztof Fidelis Subject: CASP5 oral presentations /discussion sessions, a message from John Moult Content-Type: multipart/alternative; boundary="=====================_333547375==_.ALT" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --=====================_333547375==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Predictors: All invitations for talks in the main sessions at Asilomar have been sent out. If you have not received one, I am sorry to say that means you have not been selected for an oral presentation. Please bear in mind that it is very inappropriate to equate giving a talk with 'winning', and not giving a talk with the opposite. There are over 200 groups taking part in CASP5, and less than 20 talks, so only about 10% of groups are included. There are of course many, many, more really excellent performances beyond that. As usual, there will be opportunities to contribute in other ways at the meeting, particularly in the discussions, demos and poster sessions. There is not an automatic correspondence between giving a talk and being asked to contribute a paper to the special issue of PROTEINS, but there is very limited room in the journal. To help address this problem we are launching a web site where all predictors will be able to put up descriptions of their work. We hope that this site will not only provide a means for wider distribution of CASP results, but will also be forum for constructive discussion. Details of the site will be available at the Asilomar meeting. John Moult for CASP5 organizers. --=====================_333547375==_.ALT Content-Type: text/html; charset="us-ascii" Dear Predictors:

All invitations for talks in the main sessions at Asilomar have been sent out. If you have not received one, I am sorry to say that means you have not been selected for an oral presentation. Please bear in mind that it is very inappropriate to equate giving a talk with 'winning', and not giving a talk with the opposite. There are over 200 groups taking part in CASP5, and less than 20 talks, so only about 10% of groups are included. There are of course many, many, more really excellent performances beyond that. As usual, there will be opportunities to contribute in other ways at the meeting, particularly in the discussions, demos and poster sessions.
There is not an automatic correspondence between giving a talk and being asked to contribute a paper to the special issue of PROTEINS, but there is very limited room in the journal. To help address this problem we are launching a web site where all predictors will be able to put up descriptions of their work. We hope that this site will not only provide a means for wider distribution of CASP results, but will also be forum for constructive discussion. Details of the site will be available at the Asilomar meeting.

John Moult
for CASP5 organizers.



--=====================_333547375==_.ALT-- From russell@embl-heidelberg.de Fri Nov 22 10:51:34 2002 MIME-Version: 1.0 Date: Fri, 22 Nov 2002 19:51:20 +0100 From: Rob Russell To: cc: John Moult , Anna Tramontano , Nick Grishin Subject: CASP5 invitation to speak at Asilomar Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Dear Dr Karplus: In my capacity as assessor for the CASP5 new fold category, it is my pleasure to invite you, or somebody from your group, to speak at the December meeting. We were very impressed by your overall performance bith in the new fold (NF) and fold recognition (FR) categories, so we wish you to speak about both types of predictions. Within the NF context, we were interested in your HMM method for fragment identification and subsequent assembly into tertiary structures. You also did well in the FR "analogues" and we are curious as to whether you are finding analogous whole-protein templates or assembling fragments into structures resembling known folds. You are currently scheduled to speak for 15 minutes followed by a five-minute discussion period. We will be strict regarding speakers keeping to time. The talk is currently scheduled for the 4th of December in the morning, but please be flexible. For instance, it might be necessary to move you to the 3rd, and the length of the talk may change slightly as meeting plans develop. For your information, we evaluated 13 targets during our assessment. Five of these were true new folds (NF): T0129, T0149_2 (domain 2; 203- 318), T0161, T0162_3 (114-281), T0181; and an additional eight lay on the border with fold recognition (NF/FR): T0146_1 (1-24,114-196), T0146_2 (25-113), T0146_3 (244-299), T0170, T0172_2 (116-216), T0173, T0186_3 (257-292) and T0187_1 (4-22, 250-417). Problems meant that we could not consider T0131 or T0139 during our assessment. I hope to see you in Asilomar this December. With best wishes, Rob Russell (on behalf of the CASP5 organisers) Group Leader, Structural Bioinformatics EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany Tel: +49 6221 387 473 (office) Tel: +49 6221 387 305 (lab) FAX: +49 6221 387 517 Email: russell@embl-heidelberg.de Web pages: http://www.russell.embl-heidelberg.de/ From fidelis@llnl.gov Sat Nov 23 20:46:04 2002 MIME-Version: 1.0 X-Sender: e272374@popcorn.llnl.gov Date: Sat, 23 Nov 2002 19:55:26 -0800 To: Predictor_list:; From: Krzysztof Fidelis Subject: Release of TARGET coordinates Content-Type: multipart/alternative; boundary="=====================_359807365==_.ALT" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --=====================_359807365==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CASP5 Predictors, We are now able to release at least some of the target structures. In most cases such an action must be have been cleared with target providers. We are pursuing this issue vigorously and will release additional structures as we obtain permissions. Please note that these coordinates, except for some cases listed below, have been obtained IN CONFIDENCE and are not to be further distributed. They are provided with the sole purpose of comparing your predictions with the experimental data. The following targets ARE publicly available (please use the publicly released coordinates for these targets): T0138 1m2e (1m2f) T0139 1koy T0141 1iya T0153 1mq7 T0170 1h40 T0182 1o0x T0184 1o0w T0185 1j6u T0187 1o0u * Targets T0164 and T0166 have been withdrawn from CASP5. * Targets T0158, T0163, and T0171 have not as of yet been provided. * Targets T0136 and T0162, although solved, were not released to predictors. * The structure of T0145 could not be solved, it appears to be a "natively unfolded" protein, a manuscript describing this case should appear on the target site below shortly. * For T0194 a structure of a distant homologue was obtained instead of the target one. * T0131 has been solved but the structure is unreliable. * Structures for the following targets were obtained by NMR: T0138, 139, 141, 170, 176, and 181. All of the released CASP5 target structures are available from the following site: http://predictioncenter.llnl.gov/casp5/targets/cgi/pass/download.cgi User: predictor Psswd: T@rget$ Krzysztof Fidelis for CASP5 organizers --=====================_359807365==_.ALT Content-Type: text/html; charset="us-ascii" Dear CASP5 Predictors,

We are now able to release at least some of the target structures. In most cases such an action must be have been cleared with target providers. We are pursuing this issue vigorously and will release additional structures as we obtain permissions. Please note that these coordinates, except for some cases listed below, have been obtained IN CONFIDENCE and are not to be further distributed. They are provided with the sole purpose of comparing your predictions with the experimental data.

The following targets ARE publicly available (please use the publicly released coordinates for these targets):

T0138 1m2e (1m2f)
T0139 1koy
T0141 1iya
T0153 1mq7
T0170 1h40
T0182 1o0x
T0184 1o0w
T0185 1j6u
T0187 1o0u
  • Targets T0164 and T0166 have been withdrawn from CASP5.
  • Targets T0158, T0163, and T0171 have not as of yet been provided.
  • Targets T0136 and T0162, although solved, were not released to predictors.
  • The structure of T0145 could not be solved, it appears to be a "natively unfolded" protein, a manuscript describing this case should appear on the target site below shortly.
  • For T0194 a structure of a distant homologue was obtained instead of the target one.
  • T0131 has been solved but the structure is unreliable.
  • Structures for the following targets were obtained by NMR: T0138, 139, 141, 170, 176, and 181.


All of the released CASP5 target structures are available from the following site:

http://predictioncenter.llnl.gov/casp5/targets/cgi/pass/download.cgi

User: predictor
Psswd: T@rget$

Krzysztof Fidelis
for CASP5 organizers






--=====================_359807365==_.ALT-- From fidelis@llnl.gov Mon Nov 25 19:24:41 2002 MIME-Version: 1.0 X-Sender: e272374@popcorn.llnl.gov Date: Mon, 25 Nov 2002 18:32:17 -0800 To: CASP5_Predictors:; From: Krzysztof Fidelis Subject: Additional TARGET structures released Content-Type: multipart/alternative; boundary="=====================_532920138==_.ALT" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --=====================_532920138==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Predictors, We have added structures of the following targets to our database: T0129, 130, 132, 137, 142, 146, 147, 148, 149, 150, 157, 160, and 190. They are to be found at location specified in my previous e-mail. Again, please note that these structures have been released for the sole purpose of comparing with predictions. Krzysztof Fidelis for CASP5 organizers --=====================_532920138==_.ALT Content-Type: text/html; charset="us-ascii" Dear Predictors,

We have added structures of the following targets to our database:

T0129, 130, 132, 137, 142, 146, 147, 148, 149, 150, 157, 160, and 190.

They are to be found at location specified in my previous e-mail. Again, please note that these structures have been released for the sole purpose of comparing with predictions.

Krzysztof Fidelis
for CASP5 organizers


--=====================_532920138==_.ALT-- From katye@soe.ucsc.edu Tue Nov 26 13:37:59 2002 MIME-Version: 1.0 Date: Tue, 26 Nov 2002 13:38:00 -0800 From: Katy Elliott Organization: Center for Biomolecular Science & Engineering X-Accept-Language: en To: kaf@grot.llnl.gov, yadon1@llnl.gov CC: Kevin Karplus , Rachel Karchin , learithe@cats.ucsc.edu Subject: IMPORTANT CASP5: Rachel Karchin swap with Jennie Draper Content-Type: text/plain; charset=us-ascii X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Ms. Yadon, Mr. Fidelis- This is notification that the Karplus group from UCSC will be sending Jennie Draper to CASP5 instead of Rachel Karchin. Please can you amend your records, and make sure that Ms. Draper is permitted into the conference when she arrives? We are terribly sorry for this late notice---. Please let me know if there's anything I can do on this end to make this switch easier for you. Sincerely, Katy Elliott -- Katy Elliott Administrative Manager Center for Biomolecular Science & Engineering University of California, Santa Cruz 312B Baskin Engineering Voice: (831) 459-4366 Fax: (831) 459-4829 From karplus@bray.cse.ucsc.edu Fri Nov 29 07:57:14 2002 Date: Fri, 29 Nov 2002 07:56:59 -0800 From: Kevin Karplus To: russel@embl-heidelberg.de CC: grishin@chop.swmed.edu, anna.tramontano@uniroma1.it, karplus@soe.ucsc.edu Subject: CASP5 talk I've been having some trouble putting together my talk for CASP5. I'd be glad to talk about my new-fold methods, but I looked over the structures that the CASP web sites has that are in the NF or NF/FR categories, and compared them to my predictions. Other than T0129, I didn't find anything very good to talk about. I'm not used to the standards of new-fold prediction, so I'm not sure whether things like getting a beta sheet but with the wrong topology (as in t0146_2 or t0149_2) is a success or a failure, You asked me " we are curious as to whether you are finding analogous whole-protein templates or assembling fragments into structures resembling known folds." I'm curious about that too, but it is a hard question to answer since my program treats whol-protein alignments and fragments in the same manner. It is hard for me to determine where success is coming from when I can't even discern the success. One prediction I liked when I made it was t0131, but that structure has not been released on the CASP5 website, so I've no idea whether it was good or not. I see that it was not assessed either, so I guess it is not the best target to discuss. Could you give me some hints about which targets had something in them worth discussing? (Of course, I could also just talk about my methods without giving examples from CASP, but that has not been the CASP tradition.) Thanks, Kevin Karplus From karplus@bray.cse.ucsc.edu Sat Nov 30 10:54:16 2002 Date: Sat, 30 Nov 2002 10:54:12 -0800 From: Kevin Karplus To: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu, weber@soe.ucsc.edu, learithe@cats.ucsc.edu, yael@biology.ucsc.edu, baertsch@soe.ucsc.edu, rph@soe.ucsc.edu, afyfe@soe.ucsc.edu, jcasper@soe.ucsc.edu, oscarhur@soe.ucsc.edu Subject: CASP schedule X-Sender: e272374@popcorn.llnl.gov Date: Fri, 29 Nov 2002 15:17:31 -0800 To: CASP5_Predictors:; From: Krzysztof Fidelis Subject: Meeting_Program CASP5 Meeting Program All talks in Chapel, unless otherwise noted Sunday, December 1st - Registration and Introduction 3:00 - 6:00 Registration 6:00 Dinner 7:15 The CASP5 Experiment John Moult 7:45 CASP5 Evaluation Methods Krzysztof Fidelis, Adam Zemla 8:30 CASP5 Prediction Targets Nick Grishin 9:00 Discussion 9:15 Mixer (Fred Farr Forum) Monday, December 2nd - Comparative Modeling / Fold Recognition Day 8:30 Analysis of Comparative Modeling Predictions Anna Tramontano Presentations by Comparative Modeling Groups: 9:30 G020/517 Janusz Bujnicki 9:55 G425 Ceslovas Venclovas 10:15 Break 10:40 G427 Dani Fischer 10:55 G448 Alexey Murzin 11:10 Discussion 12:00 Lunch 1:00 Livermore Prediction Center Town Hall Meeting Chair: Krzysztof Fidelis 3:00 - 6:00 Posters and Demonstrations (Merrill Hall) 5:00 HP meeting (Chapel Hall) 6:00 Dinner 7:15 Analysis of Fold Recognition Predictions Lisa Kinch, Nick Grishin Presentations by Fold Recognition Groups: 8:15 G453 Krzysztof Ginalski 8:40 G006 Leszek Rychlewski 9:05 Bar (Merrill Hall) Tuesday, December 3rd - Fold Recognition Day Presentations by Fold Recognition Groups: 8:15 G096 Paul Bates 8:30 G 110 Barry Honig 8:45 G012 Ying Xu 9:00 G450/464 Gilles Labesse Server Predictions 9:15 CAFASP3 Dani Fischer 10:00 Break 10:30 Livebench Leszek Rychlewski 11:15 G045 Arne Elofsson 11:40 G029 David Baker 12:00 Lunch 1:00 Model Database Planning Meeting Chair: Tim Hubbard 3:00 - 6:00 Posters and Demonstrations (Merrill Hall) 5:00 Ten Most Wanted (Model Survey Session - Merrill Hall) 6:00 Dinner 7:15 Discussion of Comparative Modeling and Fold Recognition 9:15 Bar (Merrill Hall) Wednesday, December 4th - New Folds Methods Day 8:15 Analysis of New Fold Results Rob Russell Presentations by New Fold Methods Groups: 9:15 G002 David Baker 9:45 G010 Jeff Skolnick 10:15 Break 10:40 G373 Charlie Brooks 11:00 G068 David Jones 11:20 G349 David Shortle 11:40 G001 Kevin Karplus 12:00 Lunch 1:00 CASP Community Meeting Chair: John Moult 3:00 - 6:00 Posters and Demonstrations (Merrill Hall) 6:00 Dinner 7:30 Secondary Structure and Contacts By CASP Patrick Aloy By EVA and CAFASP Volker Eyrich 8:30 Discussion 9:15 Bar (Merrill Hall) Thursday, December 5th 8:15 CAPRI: Protein-protein Docking Shoshana Wodak 9:15 Disorder Predictions Chair: John Moult Contributions by Keith Dunker and David Jones 10:15 Break 10:40 Ten Most Wanted Chair: Krzysztof Fidelis 12:00 Lunch 1:00 Conference Ends From fidelis@llnl.gov Wed Dec 11 14:45:24 2002 MIME-Version: 1.0 X-Sender: e272374@popcorn.llnl.gov Date: Wed, 11 Dec 2002 13:57:10 -0800 To: CASP5_Predictors:; From: Krzysztof Fidelis Subject: CASP5 Evaluation Data Content-Type: multipart/alternative; boundary="=====================_1898754073==_.ALT" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --=====================_1898754073==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CASP5 Predictors, Public release of the CASP5 evaluation data, specifically the RASMOL plots of superimposed predicted and experimental structures, requires permission from the involved parties. We are working to obtain these permissions and will make them publicly available shortly. It should be expected, however, that considerable number of structures will not be available for public viewing. Meanwhile, we are releasing a password protected site, with the majority of structures available. With few exceptions, the rest should be available with in a day or two. Please note that the confidentiality of many of these structures remains in effect and you are requested not to forward them to anyone. This includes publication of figures. I will shortly post a list of structures for which images and/or coordinates can be freely disseminated. Prediction evaluation site available to predictors only: http://predictioncenter.llnl.gov/casp5/ResultS/CASP_BROWSER/ Login: assessor P.: D@ta& Krzysztof Fidelis for CASP5 organizers --=====================_1898754073==_.ALT Content-Type: text/html; charset="us-ascii" Dear CASP5 Predictors,

Public release of the CASP5 evaluation data, specifically the RASMOL plots of superimposed predicted and experimental structures, requires permission from the involved parties.  We are working to obtain these permissions and will make them publicly available shortly. It should be expected, however, that considerable number of structures will not be available for public viewing. Meanwhile, we are releasing a password protected site, with the majority of structures available. With few exceptions, the rest should be available with in a day or two. Please note that the confidentiality of many of these structures remains in effect and you are requested not to forward them to anyone. This includes publication of figures. I will shortly post a list of structures for which images and/or coordinates can be freely disseminated. 

Prediction evaluation site available to predictors only:

http://predictioncenter.llnl.gov/casp5/ResultS/CASP_BROWSER/
Login: assessor
P.: D@ta&

Krzysztof Fidelis
for CASP5 organizers



--=====================_1898754073==_.ALT-- From russell@embl.de Thu Dec 19 11:57:43 2002 Date: Thu, 19 Dec 2002 20:57:40 +0100 (MET) To: karplus@soe.ucsc.edu Sender: From: Rob Russell Subject: We need your help assessing CASP5 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Dear Dr Karplus: This is related to your predictions in CASP5 as group SAM-T02-human (001). We are in the process of writing the paper on the New Fold assessment during CASP5 and would appreciate your help. We are trying to determine the methods used to make the best predictions. As some of you will remember from discussions during the meeting, our survey of abstracts was shown to have a number of errors in interpretation. To avoid further mistakes like this, we have decided to solicit details from the predictors directly. If you have recieved this message then you have been identified as one of the groups who did particularly well during at least one assessment scheme. We would appreciate if you could spend a few minutes filling in the questionaire below. We are on a tight deadline, so responses received after the 15th of January willl not be considered. We will send a reminder a few days before this date. It would be easiest for us if you could just edit this Email in a reply directly to me (russell@embl.de) With many thanks and best wishes for the holidays, Rob, Caroline, Alex & Patrick EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany Tel:+49 6221 387 473/305 (office/lab) FAX:+49 6221 387517 Email: russell@embl.de URL: www.russell.embl.de ----------------------------------------------------------------------- QUESTIONAIRE The targets we are considering: New Fold Targets (NF): T0129 T0149_2 T0161 T0162_3 T0181 New Fold / Fold Recognition Borderline Targets (NF/FR): T0146_1 T0146_2 T0146_3 T0172_2 T0173 T0186_3 T0187_1 T0170 Please give a concise summary of the method you tended to use for NF or NF/FR targets. 1. Would you classify your method as exclusively fold recognition (i.e always using an alignment to a template that covers most of the target sequence)? 2. Did you alter your prediction method based on some prior-classification of targets (considering only those above)? If 'YES', could you let us know how you classified the targets. 3. Does your method use secondary structure prediction? If 'YES', what method did you use? (eg. PSIpred, PHD, etc.) 4. Does your method have any manual intervention (eg. adjusting alignments, inspecting models, etc.)? If 'YES', please describe how much manual intervention was used. 5. Does your method use homologous sequence information for the target sequence? If 'YES', please desribe how. 6. Did you split target sequences into domains before predicting structure? If 'YES', what method did you use to define domains? 7. Is your method a fragment-based approach to predicting structure? If 'YES', what fragment library did you use? 8. Did you use any publically-available server to assist in your predictions? If 'YES', which servers did you use? What were they used for? (ie. screening targets, finding templates/fragments, etc.). 9. Does your method include lattice-based representations of proteins? 10.Does your method include threading-type potentials (e.g. pair-potentials, etc.) If 'YES', please describe the potentials used. 11.Does your method include steps for relaxation, optimization, minimization step? If 'YES', please describe. Please add any other information about your method that you feel is important. ----------------------------------------------------------------------- From karplus@cse.ucsc.edu Thu Dec 19 18:38:26 2002 Return-Path: Date: Thu, 19 Dec 2002 18:37:26 -0800 From: Kevin Karplus To: russell@embl.de CC: karplus@cse.ucsc.edu, rachelk@cse.ucsc.edu, weber@cse.ucsc.edu, learithe@cats.ucsc.edu, yael@biology.ucsc.edu, baertsch@cse.ucsc.edu, rph@cse.ucsc.edu, afyfe@cse.ucsc.edu, jcasper@cse.ucsc.edu, oscarhur@cse.ucsc.edu In-reply-to: <200212191957.UAA06418@tau.EMBL-Heidelberg.DE> (message from Rob Russell on Thu, 19 Dec 2002 20:57:40 +0100 (MET)) Subject: Re: We need your help assessing CASP5 Here are the answers to the new-fold questionnaire. Note: if anyone on the team wants to correct or clarify any of these answers, send mail both to me and to Rob Russell russell@embl.de > QUESTIONAIRE > > The targets we are considering: > > New Fold Targets (NF): > T0129 T0149_2 T0161 T0162_3 T0181 > > New Fold / Fold Recognition Borderline Targets (NF/FR): > T0146_1 T0146_2 T0146_3 T0172_2 T0173 > T0186_3 T0187_1 T0170 > > Please give a concise summary of the method you tended to use for NF or > NF/FR targets. > > 1. Would you classify your method as exclusively fold recognition (i.e > always using an alignment to a template that covers most of the > target sequence)? My methods were not EXCLUSIVELY fold recognition, though I always did a fold-recognition step as part of the process. > 2. Did you alter your prediction method based on some prior-classification > of targets (considering only those above)? > If 'YES', could you let us know how you classified the targets. No, I ran all targets through the same process (which hurt my performance considerably on the CM targets, where stopping after the fold-recognition step would have been much better, as evidenced by the better performance of the SAM-T02 server compared with SAM-T02-human). > 3. Does your method use secondary structure prediction? > If 'YES', what method did you use? (eg. PSIpred, PHD, etc.) Yes, we used 4 different neural nets to predict local structure, all usinga thinned SAM-T2K multiple alignment as input. The 4 networks were trained for the following predictions: STRIDE; DSSP; STR, our extended DSSP alphabet that subdivides the beta strands; and ALPHA11, based on torsion angles between adjacent CA atoms. See http://www.soe.ucsc.edu/research/compbio/SAM_T02/sam-t02-faq.html#secondary-meaning for an explanation of the alphabets. The method could be tersely described as "SAM-T02", though the ALPHA11 prediction is not currently done by the SAM-T02 web server. > 4. Does your method have any manual intervention (eg. adjusting > alignments, inspecting models, etc.)? > If 'YES', please describe how much manual intervention was used. We had extensive manual invervention on the harder problems, having to assemble the beta sheets by hand in many cases. We tended to go through a cycle of looking at the low cost models provided by undertaker, modifying the cost function (often adding constraints by hand, or modifying previously added constraints), reoptimizing, and looking at the new models. I chose the "best" few models to submit personally, though I often considered recommendations from other members of the team for their favorite models. > 5. Does your method use homologous sequence information for the target > sequence? > If 'YES', please desribe how. Most definitely. We start by building a multiple alignment of probable homologs using the SAM-T2K iterative search, then use that multiple alignment for secondary structure prediction and for building an HMM. We use the HMM (and multi-track HMMs built from it plus the output from the secondary structure predictors) to do fold recognition and to generate fragments for assembly by undertaker. > 6. Did you split target sequences into domains before predicting > structure? > If 'YES', what method did you use to define domains? We generally started from a whole-chain prediction, but in some cases we tried breaking the target up into smaller pieces and repeating the fold recognition on the pieces. These were not always domain-based---in some cases we used arbitrary overlapping pieces. > 7. Is your method a fragment-based approach to predicting structure? > If 'YES', what fragment library did you use? YES. Undertaker uses 3 sources of fragments: 1) a "generic" fragment library consisting of all 1-, 2-, 3-, and 4-residue fragments in a set of about 500 PDB files. These are indexed by the sequence of residues in the fragments. The generic residues are included to allow essentially arbitrary conformations to be in the search space, but are not relied on to produce "good" conformations. 2) a "specific" fragment library generated by fragfinder, which used a 2-track HMM (amino acids plus predicted STR) to look for fragments of length about 9 in our template library of about 7000 PDB files. We kept the top-scoring 6 fragments centered on each residue. 3) a long-fragment library (mixed with the specific library internally) consisting of gap-free segments from the alignments to templates suggested by the fold-recognition process. We generally had about 20 alignments to each of about a dozen templates included for each target. In addition to the fragments from the alignments, the whole alignments could be inserted into the conformation during the fragment assembly process, so that full fold-recognition is not really distinguishable from new-fold assembly by the program. > 8. Did you use any publically-available server to assist in your > predictions? > If 'YES', which servers did you use? What were they used for? (ie. > screening targets, finding templates/fragments, etc.). We looked at the CAFASP results manually to see whether our template selections were consistent with what other people were getting. In some cases we included the Robetta models as possible conformations to modify in our optimization process. > 9. Does your method include lattice-based representations of proteins? Nope, I have no faith in lattice-based representation. > 10.Does your method include threading-type potentials (e.g. pair-potentials, etc.) > If 'YES', please describe the potentials used. We have a cost function, but the only pairwise terms are for cysteine residues. Most of the terms in the cost function are local environment properties, especially our notions about hydrophobic burial. We did not even have a hydrogen-bonding term in the cost function, which meant we needed to add hydrogen bonds as manual constraints, to keep the sheets from being blown apart in optimization. > 11.Does your method include steps for relaxation, optimization, > minimization step? > If 'YES', please describe. I'm not sure what the difference is between "relaxation", "optimization", and "minimization". We were certainly doing a stochastic search of conformation space using a cost function. We did NOT follow this optimization with another smaller-motion optimization using a different cost function (which is what I THINK you mean by "relaxation"). > Please add any other information about your method that you feel is important. We did not cluster the conformations we generated, but looked only at the low-cost ones. Since we often had several cost functions for a given target (using different weights for the components or different manual constraints), we looked at the low-cost conformations under several different cost functions and chose which to submit manually. Info about individual targets: T0129 The first model was picked as the best scoring with no manual constraints, though helix formation was favored by the cost function. Our best model (model3) was one where we liked the packing, but did not like the way that helix5 was messed up. We did not include the robetta models in the optimization that led to models 2 and 3, though they had been considered in generating models 1 and 4. We did not divide this protein into domains, though we had thought that the first 3 helices were one subdomain. It turns out that the 4th helix should be included with them and not with the last 3 as we had thought. We did use manual constraints in all the optimizations to try to get the helices to bundle together, though model 1 was reoptimized without the manual constraints. T0149_2 (203-318) We recognized that fold-recognition had found only the N-terminal domain and tried predicting 191-318 as a separate domain. We also tried doing fold recognition for 1-200, 151-200, and 181-318. We got weak fold-recogntion matches to SCOP domain c.37.1 (the same fold as the Nterminus) for the C terminus, and conjectured a tandem repeat, but could not get this to work in undertaker. We tried adding constraints to hand-assemble the beta strands of the second domain. We tried assembling the two domains separately then joining them together. T0161 We found no homologs in the SAM-T2K iterative search, so the HMM and secondary-structure prediction were expected to be bad. We tried packing predicted strands by hand, using the Robetta models for hints. We also added straightness constraints for some predicted strands. Undertaker kept wanting to change this into a 4-helix bundle. I haven't seen the correct solution yet, so I don't know whether any of our models were in the right general direction. T0162_3 (114-281) We had no strong fold-recognition signals here, not even for the easier domains. We used the Robetta models as well as our own as starting points for optimization. We guessed at sheet topologies and added constraints. We considered trying to form a disulphide bridge C141-C157. I still haven't seen the correct structure, so I don't know whether any of our explorations were on the right track. We made no attempt to break this into domains for prediction. T0181 This is one of the ones I was asked to talk about (though I didn't know that until I was actually at CASP5, and I still haven't seen the correct structure). We had some weak fold-recognition hits, though we believed them to be too weak ro be much use for anything but super-secondary structure. We did try to use the hits to get guesses about how the predicted anti-parallel strands were linked. Our model 1 (try22-opt) was the best scoring with no manual constraints and with three differenet sets of manual constraints. Our model 2(try18-opt) was best-scoring with two other sets of manual constraints. T0146 We tried doing some subdomains: 1-80, 1-180, 120-220, 180-325. We predicted a domain boundary around 130-140 (which now seems a bit too high). We liked the looks of the robetta2 and robetta3 models, which had one big sheet, but we were not able to get a big sheet to form. By our 18th try we had the beginnings of a beta sandwich. Our model1 was heavily based on robetta's model 2. We had substantially better decoys in our set for each of the 4 domains, though none were really good. CA RMSD whole _1 _2 _3 _4 best for each 19.0241 14.4597 10.0453 14.4931 10.5645 submitted models: 1 try3-robetta2.1.60 20.1361 17.4053 12.0392 17.3951 12.6009 2 try18.3.80 21.3237 20.5213 12.8935 15.3085 14.3686 3 try20-opt-scwrl 21.6017 20.8086 12.8589 18.3672 14.3224 4 try11-al10.1.40 21.7395 17.4999 13.0246 15.7971 13.3209 5 try21.0.80 21.6111 20.4989 13.4218 15.0706 14.1969 For domain 1 (1-24,114-196), model 4 is best, model 1 second best. Real beta sheet is antiparallel 345216, with 1 coming from a distant part of the sequence. Strands 2,3, and 6 were not predicted by str neural net. Model 4 has no beta sheet here. Model 1 has one hairpin (for strands 4-5). For domain 2 (25-113), model 4 is best, model 1 second best. In real_2 the sheet is antiparallel in order 51432 and the predicted helix between 1 and 2 is only half there, to let 1 and 2 run in opposite directions. In model 1, the sheet is order 1^2v3^4v5v (so 234 are ok, but 1 needs to be moved between 4 and 5). Also 5 is almost at right angles to the sheet, not really parallel or antiparallel. In model 4, only 234 are in the anti-parallel sheet. 1 separated about the right distance but is oriented the wrong direction and 5 is well-away from the sheet. For domain 3 (244-299), model 5 is best, model 1 second best. Not much similarity between the correct structure and model 1, and secondary structure prediction is poor. Model 5 is not really much better, still having wrong secondary structure. For domain 4 (197-243 not new fold?), model 4 is best, model 1 second best. Secondary structure prediction ok, but even model 4 is not a good fit. T0172_2 (116-216) We did try a subdomain 106-222 with constraints on the two ends, to try to model the inserted domain. domain 1: We submitted one straight fold-recognition prediction (as model 3) which did the best of our models on the first domain. I was predicting that that topology of domain 1 would be 3^2^1^4^5^6^7 instead of 3^2^1^4^5^7v6^ as in 1dusA. Unfortunately, the 1dusA template was correct in the topology. I did predict that C46-C49 would be a disulphide bond (though for a while I entertained the idea that they were part of a metal-binding site. domain 2: My secondary structure prediction for domain2 was pretty good, but I was having a lot of difficulty getting the helices to pack up near the other domain. I don't think we really managed to do anything with our submitted models on this one. We did have a better decoy in our set, though it did not score well. CA RMSD whole _2 best: try4.13.25 11.3483 12.1486 model 1: try26-opt 20.8816 17.4086 model 2: try29-opt 20.9515 17.4927 model 3: T0172-1dusA.pdb incomplete model 4: try20-opt 20.9603 19.9299 T0173 We predicted a parallel topology and fairly arbitrarily tried to force the protein to be a TIM-barrel. We tried to cluster residues we believed to be part of an active site: H13,D15,D16,E44,R68,E71, D95, H144, D146,H147, H244, Q247, E271. We did not have 8 predicted strands, only 7, and fishing around for another one resulted in rather disordered structures. We had terrible secondary structure prediction for the c-terminus, missing all the strands. I have not seen the correct structure yet, so I don't know if any of our decoys that were not submitted were any good. T0186_3 (257-292) We broke this target into two domains (1-43,331-364 and 44-330). We did not see 257-292 as a separate domain. The undertaker optimization of the domains messed up the good alignments of the fold recognizer (our server did much better on this target), so that good performance on the long loop (or domain3) was impossible---the endpoints were not in the right places. T0187_1 (4-22,250-417) We tried arbitrary subdomains 1-150, 91-240, 201-350, 301-417, but none of them seem to have been able to fold, so we used them just as sources for more fragments doing fragment packing on the whole structure. We tried guessing strand topologies and adding constraints to try to get beta sheets to form, but were not particularly successful. T0170 Secondary structure prediction was pretty good, but we botched the packing of the helices. The best-fitting decoy in our whole set was the robetta model 3, though our cost function liked our models much better than it like the robetta ones. We predicted an N-terminus helix (that didn't exist) packing where the C-terminal helix should have been. From jmoult@tunc.org Sun Dec 22 05:18:28 2002 MIME-Version: 1.0 Date: Sun, 22 Dec 2002 08:18:15 -0500 From: John Moult Subject: Invitation to submit a CASP paper. X-Sender: moult@comcast.net To: karplus@soe.ucsc.edu Content-type: text/plain; charset=us-ascii; format=flowed X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Dear Kevin, I am writing to invite you to submit a paper for consideration for publication in the CASP5 special issue of PROTEINS. The organization of the issue will be similar to that of previous CASPs, with some general papers, and sections on comparative modeling, fold recognition, and new fold methods. In addition, there will a section on Servers. Your paper would be in the new fold methods section. Your paper will be thoroughly reviewed for scientific merit and relevance. As is usual for the CASP issue, the paper should focus primarily on what went right, what went wrong, and why. In particular, please address as directly and usefully as possible why it is that your results are not perfect. What are the real bottlenecks to progress with your method, and how may they be overcome? (But not too much speculation on the latter!) Because of space restrictions, please do not devote unnecessary space to methods that have already been published. Instead, do link success or failures to particular aspects of your methods. You should also pay careful attention to any specific instructions you received from the assessors for your Asilomar talk. Reviewers will be asked to check that these guidelines have been adhered to. Bear in mind that summary information will be included in the assessors' papers, and so space can be saved in the prediction papers by referring to that. If you are unsure whether relevant information will be present, please consult the relevant assessor. As you know, pictures of the experimental target structures may only be included with the agreement of the experimentalists concerned. Please check the Prediction Center list for current permissions. Please do NOT contact the experimentalists directly on this matter. The paper should occupy no more than 5 journal pages, including everything: i.e. 'occupy' means the real page increment in the table of contents. This is a very serious space restriction, and reviewers will be asked to carefully ensure that papers conform. To help you keep within the limit, here are some data on PROTEIN page layout: Column lines are about 8 words wide. There are about 60 lines in a column page. So about 960 words in a full page. Figure captions are in a smaller font: 10 words/line, 9 lines/inch. Don't forget to leave room for the headings and the references. To avoid delays, and possible omission from the issue, please check that your paper is very clearly within bounds. PROTEINS will cover the cost of a first color page, but additional ones will be charged at $500 a page. The deadline for paper submission is February 15. In response to many requests, we have set an early publication date for the special issue. Because of the resulting very tight production schedule, the submission deadline must be respected - we may be forced to omit papers that are submitted late. If this date is likely to cause any problems, please let me know now, rather than later. Papers should be submitted directly to the PROTEINS web site, being sure to select the 'CASP5' category. Please also notify me by email when your paper is submitted. Please let me know if you are willing to do this. John Moult, for CASP5 organizers. From karplus@bray.cse.ucsc.edu Sun Dec 22 09:59:42 2002 Date: Sun, 22 Dec 2002 09:58:46 -0800 From: Kevin Karplus To: jmoult@tunc.org CC: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu, weber@soe.ucsc.edu, learithe@cats.ucsc.edu, yael@biology.ucsc.edu, baertsch@soe.ucsc.edu, rph@soe.ucsc.edu, afyfe@soe.ucsc.edu, jcasper@soe.ucsc.edu, oscarhur@soe.ucsc.edu In-reply-to: <5.1.0.14.2.20021222081649.029a3d08@comcast.net> (message from John Moult on Sun, 22 Dec 2002 08:18:15 -0500) Subject: Re: Invitation to submit a CASP paper. Of course, we're willing to write a paper for Proteins---that is the "prize" for doing well in the CASP experiment. The 5-page limit will be difficult, but we'll try to keep to it. From karplus@bray.cse.ucsc.edu Tue Jan 21 10:01:07 2003 Date: Tue, 21 Jan 2003 10:01:07 -0800 From: Kevin Karplus To: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu, learithe@cats.ucsc.edu, yael@biology.ucsc.edu, jcasper@soe.ucsc.edu, rph@soe.ucsc.edu Subject: writing CASP5 paper We have until Feb 15 to get the CASP5 paper written, and I haven't even started yet! Can anybody help? Rachel is spending all her writing time on her thesis, so I can't really ask her. We have only 5 pages, and this space should be used to describe our method, and say what did and didn't work. I think that a comparison between the server (without undertaker) and hand predictions (with undertaker) is probably the best we can do. I find it interesting that the ordering of the servers in CAFASP3 and LiveBench6 is quite different---we do much better in LiveBench6. From announce-bounces@forcasp.org Sun Jan 19 21:52:35 2003 MIME-Version: 1.0 X-RocketYMMF: emelamud Date: Sun, 19 Jan 2003 21:51:13 -0800 (PST) From: Eugene Melamud To: announce@forcasp.org Content-Type: text/plain; charset=us-ascii X-Mailman-Approved-At: Mon, 20 Jan 2003 01:41:27 -0500 Subject: [Announce] Forcasp Vote Boxes are active. X-BeenThere: announce@forcasp.org X-Mailman-Version: 2.1 Precedence: list Reply-To: melamud@carb.nist.gov List-Id: FORCASP Announcements List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Sender: announce-bounces@forcasp.org X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Dear CASP Predictors, The time has come to select interesting papers for CASP5 special issue of Proteins, the voting boxes are now active. http://www.forcasp.org/ Eugene Melamud CARB _______________________________________________ Announce mailing list Announce@forcasp.org http://forcasp.org/mailman/listinfo/announce From announce-bounces@forcasp.org Tue Jan 21 21:26:32 2003 MIME-Version: 1.0 X-RocketYMMF: emelamud Date: Tue, 21 Jan 2003 21:24:28 -0800 (PST) From: Eugene Melamud To: announce@forcasp.org Content-Type: text/plain; charset=us-ascii X-Mailman-Approved-At: Wed, 22 Jan 2003 01:15:28 -0500 Subject: [Announce] Voting time is running out. X-BeenThere: announce@forcasp.org X-Mailman-Version: 2.1 Precedence: list Reply-To: editor@forcasp.org List-Id: FORCASP Announcements List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Sender: announce-bounces@forcasp.org X-SpamBouncer: 1.4 (10/07/01) X-SBNote: FROM_DAEMON/Listserv X-SBPass: No Freemail Filtering X-SBClass: Bulk Dear CASP5 Predictors: Voting for special issue CASP5 papers closes at midnight (US East coast time) on the 22nd, so please go to FORCASP and cast your votes as soon as possible. John Moult. _______________________________________________ Announce mailing list Announce@forcasp.org http://forcasp.org/mailman/listinfo/announce From yael@darwin.UCSC.EDU Thu Jan 23 14:10:34 2003 MIME-Version: 1.0 X-Authentication-Warning: darwin.UCSC.EDU: yael owned process doing -bs Date: Thu, 23 Jan 2003 14:08:25 -0800 (PST) From: yael@biology.ucsc.edu To: Kevin Karplus Subject: Re: writing CASP5 paper In-Reply-To: <200301211801.h0LI17g21746@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Hi Kevin, Sorry for not answering earlier, I am still in a process of catching up with all my e-mails. I do not think I can help with writing the paper, first I don't really think I am familiar enough with the server or undertaker and second I am just starting a new position by Manny and don't feel comfortable to work on something else right now. (BTW my paper on nucleic-acid function prediction was accepted at last to JMB and will be published probably next month). In any case I just wanted to suggest my help with going through the paper when the draft is ready or if you need me to write a paragraph on the work I am familiar with. Yael Yael Mandel-Gutfreund Department of Chemistry and Biochemistry University of California, Santa Cruz Phone : 1-831-459-5128 e-mail : yael@darwin.ucsc.edu On Tue, 21 Jan 2003, Kevin Karplus wrote: > > We have until Feb 15 to get the CASP5 paper written, and I haven't > even started yet! Can anybody help? Rachel is spending all her > writing time on her thesis, so I can't really ask her. > > We have only 5 pages, and this space should be used to describe our > method, and say what did and didn't work. I think that a comparison > between the server (without undertaker) and hand predictions (with > undertaker) is probably the best we can do. > > I find it interesting that the ordering of the servers in CAFASP3 and > LiveBench6 is quite different---we do much better in LiveBench6. > > From fidelis@llnl.gov Wed Jan 29 12:30:22 2003 MIME-Version: 1.0 X-Sender: e272374@popcorn.llnl.gov Date: Wed, 29 Jan 2003 12:24:44 -0800 To: karplus@soe.ucsc.edu From: Krzysztof Fidelis Subject: CASP5 figures Content-Type: multipart/alternative; boundary="=====================_1280847611==_.ALT" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --=====================_1280847611==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Kevin, Regarding publication, the list of targets for which we have permission to publish figures is as follows: 130, 133, 134, 138, 139, 141, 142, 146-150, 155, 163, 164, 170, 182-190 We are obtaining additional permissions from the crystallographers. Please let me know if there are figures of targets other than the ones listed above that you would like to include. If there are reasons for including a structure that are of particular significance and which could be used to argue for obtaining publication permission, please let me know as well. Krzysztof --=====================_1280847611==_.ALT Content-Type: text/html; charset="us-ascii" Dear Kevin,

Regarding publication, the list of targets for which we have permission to publish figures is as follows:

130, 133, 134, 138, 139, 141, 142, 146-150, 155, 163, 164, 170, 182-190

We are obtaining additional permissions from the crystallographers. Please let me know if there are figures of targets other than the ones listed above that you would like to include. If there are reasons for including a structure that are of particular significance and which could be used to argue for obtaining publication permission, please let me know as well.

Krzysztof

--=====================_1280847611==_.ALT-- From karplus@bray.cse.ucsc.edu Wed Jan 29 12:48:32 2003 Date: Wed, 29 Jan 2003 12:48:33 -0800 From: Kevin Karplus To: fidelis@llnl.gov CC: karplus@soe.ucsc.edu In-reply-to: <5.1.0.14.2.20030129122357.02e86030@popcorn.llnl.gov> (message from Krzysztof Fidelis on Wed, 29 Jan 2003 12:24:44 -0800) Subject: Re: CASP5 figures At CASP I was asked to talk about T0129 and T0181, but these don't appear on the list. T0135 would also be nice to talk about. I can probably work around whatever restrictions there are on showing the proteins, but it is a bit annoying. From nobody@carbns.umbi.umd.edu Fri Jan 17 08:02:02 2003 MIME-Version: 1.0 From: "Announcements" To: karplus@soe.ucsc.edu Reply-To: Announcements Organization: Announcements List: announce List-Archive: http://www.forcasp.org/cgi-bin/mojo/mojo.cgi?f=archive&l=announce List-ID: 20030117115043 List-Owner: List-Subscribe: http://www.forcasp.org/cgi-bin/mojo/mojo.cgi?f=s&l=announce List-Unsubscribe: http://www.forcasp.org/cgi-bin/mojo/mojo.cgi?f=u&l=announce List-URL: http://www.forcasp.org/cgi-bin/mojo/mojo.cgi?l=announce List-Software: Mojo Mail 2.7.1 Precedence: list X-Priority: 3 Subject: Voting on Special Issue papers this Monday. Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Date: Fri, 17 Jan 2003 11:50:50 -0500 (EST) X-SpamBouncer: 1.4 (10/07/01) X-SBNote: From Admin X-SBNote: FROM_DAEMON/Listserv X-SBPass: No Freemail Filtering X-SBClass: Admin Dear CASP Predictors: A reminder that voting for papers to include in the CASP5 special of issue of proteins will take place next Monday through Wednesday. Log-on to FORCASP in that timeframe and caste your votes! There have been some comments added to the abstracts this week, mostly more information provided by the authors, some times praising their own methods a little blatantly. Still a couple of days left to get in there and beef up your own abstract, or comment on other people's, thus influencing the voting. There has also been a little discussion about availability of the results. As pointed out there, the summary tables are available. Bear in mind you are voting for interesting methods that show promise, not necessarily outright winners in this CASP. John Moult. -- To unsubscribe from: Announcements, just follow this link: http://www.forcasp.org/cgi-bin/mojo/mojo.cgi?f=u&l=announce&e=karplus@soe.ucsc.edu&p=6003 Click this link, or copy and paste the address into your browser. FORCASP: http://www.forcasp.org From jmoult@tunc.org Mon Feb 17 13:51:09 2003 MIME-Version: 1.0 Date: Mon, 17 Feb 2003 16:51:01 -0500 From: John Moult Subject: Re: CASP paper reviewing In-reply-to: <200302172136.h1HLaoa12199@bray.cse.ucsc.edu> X-Sender: moult@comcast.net To: Kevin Karplus Content-type: text/plain; charset=us-ascii; format=flowed X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Kevin: Thanks for the response. Actually, I was three emails away from asking you the status of your paper. As you know, the deadline was a couple of days ago, and the publication schedule is really tight. When can we expect the manuscript? Sorry to hear you are stranded in DC . Out here in Rockville, I have given up trying to dig out for today. Hopefully rejoin civilization tomorrow. john. At 01:36 PM 2/17/2003 -0800, you wrote: >I would be glad to review some CASP5 papers, but I haven't had time to >even START writing mine yet, so maybe I'd better not take on any more >responsibilities until I get that cleared. From karplus@bray.cse.ucsc.edu Mon Feb 17 14:34:02 2003 Date: Mon, 17 Feb 2003 14:34:05 -0800 From: Kevin Karplus To: karplus@soe.ucsc.edu In-reply-to: <5.1.0.14.2.20030217164734.03a28080@pop.earthlink.net> (message from John Moult on Mon, 17 Feb 2003 16:51:01 -0500) Subject: Re: CASP paper reviewing copy of mail to jmoult@tunc.org It will take me a couple of weeks---I have been grossly overloaded this quarter with administrative and teaching tasks. Our quarter started Jan 2 and I had to get an NSF proposal out before I could concentrate on the CASP paper. I've been having some trouble figuring out what to say in the paper, because the few examples I did well on in new-fold recognition are ones we aren't allowed to show (as far as I can tell---I'm really having difficulty figuring out which ones I did "well" on in the new-fold area). I can talk about the method we used, and why it failed on the comparative modeling cases, but I'm finding it difficult to say much about what went right. I have not had the time to really dig through the data and try to salvage a nugget from the piles of junk. I was hoping that the assessors and the numeric CASP results would provide some guidance, but I've not found them particularly informative this year. Kevin From jmoult@tunc.org Mon Feb 17 15:09:15 2003 MIME-Version: 1.0 Date: Mon, 17 Feb 2003 18:08:50 -0500 From: John Moult Subject: Guidelines for CASP paper reviewing X-Sender: moult@comcast.net To: batesp@cancer.org.uk, "Janusz M. Bujnicki" , venclovas@llnl.gov, dfischer@cs.bgu.ac.il, agm@mrc-lmb.cam.ac.uk, K.Ginalski@icm.edu.pl, leszek@bioinfo.pl, Barry Honig , dabaker@u.washington.edu, skolnick@buffalo.edu, David Jones , David Shortle , karplus@soe.ucsc.edu, bystrc@rpi.edu, rost@columbia.edu, arne@sbc.su.se, dunker@mail.wsu.edu Cc: th@sanger.ac.uk, anna.tramontano@uniroma1.it Content-type: text/plain; charset=us-ascii; format=flowed X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Dear CASP Paper Reviewers: The general guide lines for reviewing CASP papers are as follows: Papers should focus primarily on what went right, what went wrong, and why. Authors are asked to particularly address why it is their results are not perfect, and to consider the real bottlenecks to progress and how they may eventually be overcome. Excessive space should not be devoted to methods that have already been published. However, successes or failures should be linked to aspects of the methods. Some authors may have received specific instructions on what to cover from the assessors. If you are uncertain about aspects of coverage, please email me. As you know, space is very limited, and so reviewers are asked to check that page limits have been adhered to. The default is is 5 pages, with the following exceptions: Bujnicki, Venclovas: 8 (journal) pages. Ginalski: 9 pages Baker, Skolnick: 10 pages CAFASP, Livebench, EVA: 7 pages. Dunker: 7 pages. Let me know if any of this is not clear, or your need more information. John Moult. From jmoult@tunc.org Mon Feb 17 15:13:13 2003 MIME-Version: 1.0 Date: Mon, 17 Feb 2003 18:13:05 -0500 From: John Moult Subject: Re: CASP paper reviewing In-reply-to: <200302172233.h1HMXfP12390@bray.cse.ucsc.edu> X-Sender: moult@comcast.net To: Kevin Karplus Cc: th@sanger.ac.uk Content-type: text/plain; charset=us-ascii; format=flowed X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Kevin: OK, extended until March 3. BUT - please, please let's make that the REAL deadline. You might email Rob Russell to get his take on what you did well on. we may be able to clear a couple more of the targets for pictures in a day or two. John. At 02:33 PM 2/17/2003 -0800, you wrote: >It will take me a couple of weeks---I have been grossly overloaded this >quarter with administrative and teaching tasks. Our quarter started >Jan 2 and I had to get an NSF proposal out before I could concentrate >on the CASP paper. > >I've been having some trouble figuring out what to say in the paper, >because the few examples I did well on in new-fold recognition are >ones we aren't allowed to show (as far as I can tell---I'm really >having difficulty figuring out which ones I did "well" on in the >new-fold area). I can talk about the method we used, and why it >failed on the comparative modeling cases, but I'm finding it difficult >to say much about what went right. I have not had the time to really >dig through the data and try to salvage a nugget from the piles of junk. >I was hoping that the assessors and the numeric CASP results would >provide some guidance, but I've not found them particularly >informative this year. > >Kevin From karplus@bray.cse.ucsc.edu Mon Feb 17 15:56:42 2003 Date: Mon, 17 Feb 2003 15:52:44 -0800 From: Kevin Karplus To: russell@embl-heidelberg.de CC: karplus@soe.ucsc.edu Subject: help with my CASP5 paper I've missed the deadline for my CASP5 paper, because I've been swamped with other work, and because I have been having a hard time figuring out what to talk about. I've been given a short extension. Can you give me some suggestions about what seems to have worked for my FR(A)/NF predictions? Last time I looked, the only half-decent results were for structures we couldn't show. I'll have no trouble saying what went WRONG with my method, but I'm having a much harder time figuring out what to say about what went right with the SAM-T02-human predictions. Thanks, Kevin Karplus From karplus@bray.cse.ucsc.edu Sat Feb 22 17:32:34 2003 Date: Sat, 22 Feb 2003 17:32:37 -0800 From: Kevin Karplus To: adamz@llnl.gov, fidelis@llnl.gov CC: jmoult@tunc.org, th@sanger.ac.uk, karplus@soe.ucsc.edu Subject: CASP5 results I've been trying to get my CASP5 paper finished, but been stymied by the unavailability of the graphical results. I tried clicking on "graphical results" on http://predictioncenter.llnl.gov/casp5/pubResultS/CASP_BROWSER/casp5-browsers.cgi and got Not Found The requested URL /casp5/pubResultS/CASP_PLOTS/summary_gdt.html was not found on this server. I tried looking at the results all proteins for group 001 and got http://predictioncenter.llnl.gov/casp5/pubResultS/CASP_BROWSER/3d-browser/3d_res.cgi The results of the evaluation of prediction(s) Number of selected predictions: 0 The results are sorted by: TARGET -> GDT_TS -> CRMSCA(ALL_ATOMS) But I had selected all predictions! Either the web pages don't work with Netscape or there is something wrong with the server (or there is something so wrong with the human interface that I can't figure out how to use it). I could go into individual targets with the non-interactive pages, but all attempts to get to any of the graphical outputs resulted in messages like Not Found The requested URL /casp5/pubResultS/CASP_BROWSER/graphs/LCS/T0184TS189_2.T0184_1.html was not found on this server. I was hoping to do some comparison between my server and my hand method (already a difficult task on the CASP5 results pages, since there seems to be no way to compare two groups without a lot of flipping back and forth between pages). But if I can't even see the results for one of the groups, I don't know how I'm going to write about what went right and what went wrong. Kevin Karplus From adamz@bialko.llnl.gov Sat Feb 22 18:43:37 2003 Date: Sat, 22 Feb 2003 18:43:37 -0800 (PST) From: Adam ZEMLA To: Kevin Karplus Subject: Re: CASP5 results Cc: adamz@llnl.gov X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Hi Kevin, sorry but I cannot help you. About a year ago I moved to bioinformatics group. I was running CASP5, but after the meeting in Asilomar the full responsibility for maintaining CASP's websites and data is Krzysztof's who has funding for CASP to do this. So please address all concerns/requests directly to K.F. I hope Krzysztof will help you. Best regards, Adam *********************************************************************** Adam Zemla, Ph.D. | E-mail: adamz@llnl.gov Biology and Biotechnology Research Program | Phone: (925) 423-5571 Lawrence Livermore National Laboratory, L-448 | Fax: (925) 422-2133 7000 East Ave., Livermore, CA 94550, USA | Bldg: 3751, Room: 109 *********************************************************************** From russell@embl-heidelberg.de Mon Feb 24 09:23:32 2003 MIME-Version: 1.0 Date: Mon, 24 Feb 2003 18:28:18 +0100 (CET) From: Rob Russell To: Kevin Karplus cc: Patrick Aloy , Caroline Hadley , Alexander Stark Subject: Re: help with my CASP5 paper In-Reply-To: <200302172352.h1HNqi312677@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Kevin, [I've CCed my group here in case they want to add something. Guys feel free.] First of all, I must congratulate you on your outstanding humility. Certain others have been rather the opposite: insisting that they had done good predictions when they clearly hadn't. Second, what we had in mind with your paper was mostly to discuss the new approach to fragment generation. The main thing we noted, as we discussed during the questions at Asilomar, was that we tended to score you down on our "fold right/wrong" criteria. Inspection showed that this was due mostly to identification of correct fragments, but not the right fold, this was similar to results from two of the servers. We did, however, think you did a good job at T0129 and T0181. My notes are: T0129 (NF): HI0817 from H. influenzae >From the paper: This protein contains seven alpha-helices. The first four and the last three form separate bundles (N- and C- terminal bundle) separated by a long, essentially extended crossover loop between helices 4 & 5 (Figure 1A). An additional noteworthy feature is another extended loop segment connecting helices 6 & 7. Inspection of the results showed this target to be difficult when considered as a whole, with just one group getting the overall fold right. The best predictions were models 4, 1 & 3 from the Baker group (002), which are all variants on a theme that is essentially correct (Figure 1B) apart from minor alterations in the N-terminal bundle, where helices 3 & 4 are swapped. Both extended loops were predicted, but by far the most impressive aspect of these predictions is the correct relative orientation of the two sub-domains. Many other groups made good predictions of the N- and C- terminal bundles, but did not get the relative orientation correct. Good examples of this come from the Jones-NewFold (068) and Doniach (401) groups (Figure 1C & D), both of whom like several other groups predicted a largely correct structure for the extended linker region. My notes: 001 T0129TS001_3 TS T C D I G L 12.84 100.0 0.0755 26.77 70.70 GOOD 3/4 helices N-terminus right C-terminus partly right (SS poorer) Here, 20-49 fit pretty well from the N-terminus, and residues 96-168 form a three "helical" bundle that is mostly right, but distorted and residues 98-114 should be a helix and not an extended piece as you have. You were among the groups getting part points for predicting parts of the two sub-domains right. T0181 (NF) YH07 from S. cerevisiae >From the paper: The N-terminus of this protein (residues 1-95) consists of a four-stranded _-meander (i.e. strand order 1234) with four _-helices packing against one side; two helices are inserted between strands 2 & 3, and the other two lie after strand 4 in the sequence (Figure 5A). The C-terminus (96-111) consists of something resembling a short, three-stranded _-meander, though main-chain hydrogen bonding does not define any strands here. The best prediction came from the Skolnick-Kolinski group (010) who predicted the overall trace of the N-terminal half of the protein correctly, with a swap of strands 1 & 2 and the substitution of strands 3 & 4 by a helix/loop segment (Figure 5B). Other good predictions were made by the SAM-T02-Human (001; Figure 5C), Samudrala-NewFold (051; Figure 5D) as well as the PROTINFO-AB server (140). The Jones-NewFold (068) and ORNL-PROSPECT (012) groups also predicted features well, the latter notably being one of a few that predicted the entire sheet topology correctly, despite differences in the rest of the structure. 001 T0181TS001_2 TS 10.23 100.0 0.0922 30.63 71.30 GOOD, C-term. wrong, sheet 123 helix packing ok Here residues 1-50 (your model) are basically right, though the strand at 45-50 should really form a third member of the sheet (order 1-2-3, with the N-terminal strands between residues 5 and 20). Beyond this, my problem is that *I* can't see the www site stuff now either. If you want some more details, it is probably best to contact Adam Zemla directly. His phone number is +1 925 423 5571; he is, how can I put it delicately, terrible at answering Emails. All the best, and good luck, R. Rob Russell, Group Leader, Structural Bioinformatics EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany Tel:+49 6221 387 473/305 (office/lab) FAX:+49 6221 387517 Email: russell@embl.de URL: www.russell.embl.de On Mon, 17 Feb 2003, Kevin Karplus wrote: > > I've missed the deadline for my CASP5 paper, because I've been swamped > with other work, and because I have been having a hard time figuring > out what to talk about. I've been given a short extension. > > Can you give me some suggestions about what seems to have worked for > my FR(A)/NF predictions? Last time I looked, the only half-decent > results were for structures we couldn't show. > > I'll have no trouble saying what went WRONG with my method, but I'm > having a much harder time figuring out what to say about what went > right with the SAM-T02-human predictions. > > Thanks, > > Kevin Karplus > From karplus@bray.cse.ucsc.edu Tue Feb 25 10:47:02 2003 Date: Tue, 25 Feb 2003 10:44:57 -0800 From: Kevin Karplus To: russell@embl-heidelberg.de CC: aloy@embl.de, hadley@embl-heidelberg.de, alstark@embl-heidelberg.de, karplus@soe.ucsc.edu In-reply-to: (message from Rob Russell on Mon, 24 Feb 2003 18:28:18 +0100 (CET)) Subject: Re: help with my CASP5 paper Thanks for the help. I'll try to say something about T0129 and T0181. I was also thinking of talking about T0130, which was the protein that all the speakers talked about (in fold recognition). I was also thinking of talking about T0135 which was a FR(A) target that I think we did well on. I was going to mention T0139, which was (properly) withdrawn from CASP, since a picture of the protein was published before the deadline. Adam Zemla no longer works for the group that maintains the CASP5 web site. Krzysztof Fidelis is trying to fix the site. From karplus@bray.cse.ucsc.edu Tue Feb 25 16:09:29 2003 Date: Tue, 25 Feb 2003 16:09:33 -0800 From: Kevin Karplus To: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu, learithe@cats.ucsc.edu, yael@biology.ucsc.edu, jcasper@soe.ucsc.edu, rph@soe.ucsc.edu Subject: casp5 paper The CASP5 paper is way overdue. I managed to get an extension to Monday 3 march, but it still isn't finished. If anyone can help, either with comments on the existing text or with paragraphs that I can add, please do so. The existing text is in /projects/compbio/papers/protein-structure/casp5/casp5-prosfg/ Thanks, Kevin From jcasper@baa.cse.ucsc.edu Tue Feb 25 16:44:21 2003 MIME-Version: 1.0 Date: Tue, 25 Feb 2003 16:44:04 -0800 (PST) From: Jonathan Casper To: Kevin Karplus cc: rachelk@soe.ucsc.edu, , , , Subject: Re: casp5 paper In-Reply-To: <200302260009.h1Q09Xv06110@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-UCSC-CATS-MailScanner: Found to be clean X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK I haven't seen too much yet, but there's a problem with the author names. Mark Diekhans is only partway on the page, and Richary Hughey was completely lost. -Jonathan On Tue, 25 Feb 2003, Kevin Karplus wrote: > > The CASP5 paper is way overdue. I managed to get an extension to > Monday 3 march, but it still isn't finished. > > If anyone can help, either with comments on the existing text or with > paragraphs that I can add, please do so. > > The existing text is in > /projects/compbio/papers/protein-structure/casp5/casp5-prosfg/ > > Thanks, > > Kevin > From karplus@bray.cse.ucsc.edu Tue Feb 25 16:48:39 2003 Date: Tue, 25 Feb 2003 16:48:43 -0800 From: Kevin Karplus To: jcasper@soe.ucsc.edu CC: karplus@soe.ucsc.edu In-reply-to: (message from Jonathan Casper on Tue, 25 Feb 2003 16:44:04 -0800 (PST)) Subject: Re: casp5 paper Thanks---fixing the author list was pretty trivial. I've not looked much at the formatting of the paper. From russell@embl-heidelberg.de Wed Feb 26 01:07:35 2003 MIME-Version: 1.0 Date: Wed, 26 Feb 2003 10:12:30 +0100 (CET) From: Rob Russell To: Kevin Karplus cc: "aloy@embl.de" , "hadley@embl-heidelberg.de" , "alstark@embl-heidelberg.de" Subject: Re: help with my CASP5 paper In-Reply-To: <200302251844.h1PIivD03576@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK > Thanks for the help. I'll try to say something about T0129 and T0181. > > I was also thinking of talking about T0130, which was the protein that > all the speakers talked about (in fold recognition). I was also > thinking of talking about T0135 which was a FR(A) target that I think > we did well on. I was going to mention T0139, which was (properly) > withdrawn from CASP, since a picture of the protein was published > before the deadline. I think in principle these are fine. You'd have to speak to Nick Grishin about 130 and 135. For 139 I had you down as "spot-on" (so this would have been two points, had the target not been withdrawn), so if you really did not use the template or the thing it was supposedly similar to (discussed in the paper, according to Alexey), then well-done. I would be cautious not to overstate your success in light of the early publication. Good luck with the paper and best wishes, Rob From karplus@bray.cse.ucsc.edu Wed Feb 26 12:38:08 2003 Date: Wed, 26 Feb 2003 12:35:54 -0800 From: Kevin Karplus To: russell@embl-heidelberg.de CC: aloy@embl.de, hadley@embl-heidelberg.de, alstark@embl-heidelberg.de, karplus@soe.ucsc.edu In-reply-to: (message from Rob Russell on Wed, 26 Feb 2003 10:12:30 +0100 (CET)) Subject: Re: help with my CASP5 paper I did cheat on t139, looking at the picture and trying to reverse engineer some constraints from the picture. I was planning to say that I had cheated on it, but even a few not-very-accurate constraints were quite helpful in getting a better solution. From yael@darwin.UCSC.EDU Wed Feb 26 15:04:18 2003 MIME-Version: 1.0 X-Authentication-Warning: darwin.UCSC.EDU: yael owned process doing -bs Date: Wed, 26 Feb 2003 15:01:54 -0800 (PST) From: yael@biology.ucsc.edu To: Kevin Karplus Subject: Re: casp5 paper In-Reply-To: <200302260009.h1Q09Xv06110@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Hi Kevin, I am sorry, I just finished reading the paper now. I have quite a few comments (I was looking at the pdf so I have them on paper) but I am not sure if you have a new version by now. I haven't really read other casp papers before but in general I thought that the paper sounds too informal (more like a talk) e.g. in the into parag 3 "we decided (perhaps unwisely...". Also I think the into should be more positive. Yael Yael Mandel-Gutfreund Department of Chemistry and Biochemistry University of California, Santa Cruz Phone : 1-831-459-5128 e-mail : yael@darwin.ucsc.edu On Tue, 25 Feb 2003, Kevin Karplus wrote: > > The CASP5 paper is way overdue. I managed to get an extension to > Monday 3 march, but it still isn't finished. > > If anyone can help, either with comments on the existing text or with > paragraphs that I can add, please do so. > > The existing text is in > /projects/compbio/papers/protein-structure/casp5/casp5-prosfg/ > > Thanks, > > Kevin > > From karplus@bray.cse.ucsc.edu Wed Feb 26 16:14:16 2003 Date: Wed, 26 Feb 2003 16:14:20 -0800 From: Kevin Karplus To: yael@biology.ucsc.edu CC: karplus@soe.ucsc.edu In-reply-to: (yael@biology.ucsc.edu) Subject: Re: casp5 paper I've been too busy today to get anything done on the paper---much less a new draft. Please bring me any comments you have! From yael@darwin.UCSC.EDU Wed Feb 26 21:51:01 2003 MIME-Version: 1.0 X-Authentication-Warning: darwin.UCSC.EDU: yael owned process doing -bs Date: Wed, 26 Feb 2003 21:48:36 -0800 (PST) From: yael@biology.ucsc.edu To: Kevin Karplus Subject: Re: casp5 paper In-Reply-To: <200302270014.h1R0EKK12458@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Sorry I saw your message only after I got home. I will come by tomorrow and bring you my comments. Yael Yael Mandel-Gutfreund Department of Chemistry and Biochemistry University of California, Santa Cruz Phone : 1-831-459-5128 e-mail : yael@darwin.ucsc.edu On Wed, 26 Feb 2003, Kevin Karplus wrote: > I've been too busy today to get anything done on the paper---much less > a new draft. Please bring me any comments you have! > > From karplus@bray.cse.ucsc.edu Thu Feb 27 18:03:18 2003 Date: Thu, 27 Feb 2003 18:03:16 -0800 From: Kevin Karplus To: rachelk@soe.ucsc.edu CC: karplus@soe.ucsc.edu In-reply-to: <15966.37395.117028.939448@grunt.cse.ucsc.edu> (message from Rachel Karchin on Thu, 27 Feb 2003 14:32:51 -0800) Subject: Re: casp5 paper Thanks, I saved your file as pcp/protein-structure/casp5/casp5-prosfg/rachel-comments.tex I'm too fried to look at it tonight, but will try to incorporate your comments and Yael's tomorrow. Kevin From fidelis@llnl.gov Fri Feb 28 15:45:28 2003 MIME-Version: 1.0 X-Sender: e272374@popcorn.llnl.gov Date: Fri, 28 Feb 2003 15:31:00 -0800 To: David.Jones@cs.ucl.ac.uk, leszek@bioinfo.pl, bystrc@rpi.edu, dfischer@cs.bgu.ac.il, karplus@soe.ucsc.edu, iamb@genesilico.pl, venclovas1@llnl.gov, kginal@bioinfo.pl, skolnick@danforthcenter.org, dunker@mail.wsu.edu, bh6@columbia.edu, agm@mrc-lmb.cam.ac.uk, lkinch@chop.swmed.edu, grishin@chop.swmed.edu, anna.tramontano@uniroma1.it, russell@embl.de, jmoult@tunc.org, rost@columbia.edu, contrera@cancer.org.uk, arne@sbc.su.se, dunker@disorder.chem.wsu.edu, dshortl1@jhmi.edu, batesp@cancer.org.uk From: Krzysztof Fidelis Subject: Update on CASP5 target figures permissions Content-Type: multipart/alternative; boundary="=====================_-411059242==_.ALT" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --=====================_-411059242==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CASP5 Authors, We have a definitive "no" on publication of figures for targets 136 and 173. Answers for the following targets are still pending: 135, 140, 151, 181. Krzysztof Fidelis for CASP5 organizers --=====================_-411059242==_.ALT Content-Type: text/html; charset="us-ascii" Dear CASP5 Authors,

We have a definitive "no" on publication of figures for targets 136 and 173. Answers for the following targets are still pending: 135, 140, 151, 181.

Krzysztof Fidelis
for CASP5 organizers
--=====================_-411059242==_.ALT-- From gavin@gavinwelch.com Fri Feb 28 17:00:48 2003 MIME-Version: 1.0 From: "gavin" To: Subject: if i can be of some help Date: Fri, 28 Feb 2003 17:00:23 -0800 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000C_01C2DF4A.EF30C540" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK This is a multi-part message in MIME format. ------=_NextPart_000_000C_01C2DF4A.EF30C540 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi professor.. You mentioned in class the paper you were writing, and you also said something about us helping you with it. If you were serious, I am aware of your time constraints and would be willing to help. I know very little about bioinformatics, and my writing style appeals only to me I think.but I will do what I can to lend a hand on any of your tasks. Gavin ------=_NextPart_000_000C_01C2DF4A.EF30C540 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi professor..

 

You mentioned in class the paper you were writing, = and you also said something about us helping you with = it.

 

If you were serious, I am aware of your time = constraints and would be willing to help.  I know very little about bioinformatics, and my = writing style appeals only to me I think…but I will do what I can to lend a hand = on any of your tasks.

 

Gavin =

 

------=_NextPart_000_000C_01C2DF4A.EF30C540-- From karplus@bray.cse.ucsc.edu Fri Feb 28 17:15:28 2003 Date: Fri, 28 Feb 2003 17:15:33 -0800 From: Kevin Karplus To: gavin@gavinwelch.com CC: karplus@soe.ucsc.edu In-reply-to: <000b01c2df8d$fd540540$0100a8c0@mephisto> (gavin@gavinwelch.com) Subject: Re: if i can be of some help Thanks, You can find the PDF file for the current draft in http://www.soe.ucsc.edu/~karplus/casp5/casp5.pdf Just e-mail me comments that you have on the draft---attachments are too messy to deal with when I'm working across multiple computers. From karplus@bray.cse.ucsc.edu Fri Feb 28 17:55:57 2003 Date: Fri, 28 Feb 2003 17:56:03 -0800 From: Kevin Karplus To: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu, learithe@cats.ucsc.edu, yael@biology.ucsc.edu, jcasper@soe.ucsc.edu, rph@soe.ucsc.edu Subject: casp5 paper first draft done I've finished the first draft of the CASP5 paper and begun some second-draft revisions based on comments from the half-finished draft. The paper may be a bit too long, but I'll let the referees tell me that. Please give me comments on the paper this weekend, as I have to submit it on Monday. The paper can be found in /projects/compbio/papers/protein-structure/casp5/casp5-prosfg/casp5.pdf or, equivalently, http://www.soe.ucsc.edu/~karplus/casp5/casp5.pdf From yael@darwin.UCSC.EDU Sun Mar 2 22:27:27 2003 MIME-Version: 1.0 X-Authentication-Warning: darwin.UCSC.EDU: yael owned process doing -bs Date: Sun, 2 Mar 2003 22:25:00 -0800 (PST) From: yael@biology.ucsc.edu To: Kevin Karplus Subject: Re: casp5 paper first draft done In-Reply-To: <200303010156.h211u3727681@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK Hi Kevin, Sorry in the end we went out last night and were out all day today so I got to see your e-mail only this evening. I will read it right now and let you know later tonight if I have any critical comments. Yael Yael Mandel-Gutfreund Department of Chemistry and Biochemistry University of California, Santa Cruz Phone : 1-831-459-5128 e-mail : yael@darwin.ucsc.edu On Fri, 28 Feb 2003, Kevin Karplus wrote: > > I've finished the first draft of the CASP5 paper and begun some > second-draft revisions based on comments from the half-finished draft. > The paper may be a bit too long, but I'll let the referees tell me > that. > > Please give me comments on the paper this weekend, as I have to submit > it on Monday. > > The paper can be found in > /projects/compbio/papers/protein-structure/casp5/casp5-prosfg/casp5.pdf > or, equivalently, > http://www.soe.ucsc.edu/~karplus/casp5/casp5.pdf > > From gavin@gavinwelch.com Mon Mar 3 12:03:35 2003 MIME-Version: 1.0 From: "gavin" To: "'Kevin Karplus'" Subject: RE: if i can be of some help Date: Mon, 3 Mar 2003 12:03:32 -0800 Content-Type: text/plain; charset="us-ascii" X-Priority: 3 (Normal) X-MSMail-Priority: Normal In-Reply-To: <200303010115.h211FXu27544@bray.cse.ucsc.edu> Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Wow...while it was very interesting to me, Im afraid it wont be very useful to you. The terminology and concepts that you use are well out of my depth. All I can comment on is some trivial stuff that most likely makes no difference to you paper, but I will forward next. Thanks for letting me look at it..I am, at least, starting to realize what it is you are up to :) g -----Original Message----- From: Kevin Karplus [mailto:karplus@soe.ucsc.edu] Sent: Friday, February 28, 2003 5:16 PM To: gavin@gavinwelch.com Cc: karplus@soe.ucsc.edu Subject: Re: if i can be of some help Thanks, You can find the PDF file for the current draft in http://www.soe.ucsc.edu/~karplus/casp5/casp5.pdf Just e-mail me comments that you have on the draft---attachments are too messy to deal with when I'm working across multiple computers. From gavin@gavinwelch.com Mon Mar 3 13:21:50 2003 MIME-Version: 1.0 From: "gavin" To: "'Kevin Karplus'" Subject: RE: if i can be of some help Date: Mon, 3 Mar 2003 13:21:48 -0800 Content-Type: text/plain; charset="us-ascii" X-Priority: 3 (Normal) X-MSMail-Priority: Normal In-Reply-To: <200303010115.h211FXu27544@bray.cse.ucsc.edu> Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-SpamBouncer: 1.4 (10/07/01) X-SBPass: No Freemail Filtering X-SBClass: OK Ok... I am highly skeptical that this will be of use to you...and I just hope I am not wasting your already scarce time. That said, here goes. 2.1 paragraph 2 sentence 2 ...can you say directly represent instead of re3present directly 2.2 paragraph 1 sentence 1 since you have a colon with comma seperated list, can you say exactly matching, very short... 2.2 paragraph 4 sentence 1 this sentence confused me a little..after "Undertaker also has oeprators for repositioning subtrees I am expecting a list, and I am not sure if there is a relationship between jiggling and trying to find the optimal placement... 2.3 paragraph 2 sentence 2 is comma necessary? 2.4 para 2 sent 1 Should yousay the basic cost functions can also... 2,4 p 2 s 2 and 3 should these 2 sentences be switched? 2.4 p 3 s 2 do you want to say "the number of atoms within a given radius for each residue... 2.4 p 6 s 1 important, basic? 2.4 p 6 s last This sentence last? 3 p 1 s last comma aftyer For the difficult targets, 3 p 3 s 2 should you say "This is not surprising, given... 3.1 p 1 s 1 what we thought were? 3.1 p2 s 2 We mentally partitioned it? 3.3 p 1 s 2 can you say "Only our fold-recognition ... 3.3 p2 s 1 do you want to end sentence after assembled 3.3 p2 s2 sheets, resulted ? 3.3 p2 s3 I dont really get this sentence. Typo? Hope this helps.. The paper is terrific.. Good luck g -----Original Message----- From: Kevin Karplus [mailto:karplus@soe.ucsc.edu] Sent: Friday, February 28, 2003 5:16 PM To: gavin@gavinwelch.com Cc: karplus@soe.ucsc.edu Subject: Re: if i can be of some help Thanks, You can find the PDF file for the current draft in http://www.soe.ucsc.edu/~karplus/casp5/casp5.pdf Just e-mail me comments that you have on the draft---attachments are too messy to deal with when I'm working across multiple computers. From karplus@bray.cse.ucsc.edu Mon Mar 3 15:54:41 2003 Date: Mon, 3 Mar 2003 15:54:45 -0800 From: Kevin Karplus To: gavin@gavinwelch.com CC: karplus@soe.ucsc.edu Subject: [gavin@gavinwelch.com: RE: if i can be of some help] Thanks---I used several of your suggestions. Here is what I did with each comment: 2.1 paragraph 2 sentence 2 ...can you say directly represent instead of represent directly Nope, that would split an infinitive without a strong reason to do so. 2.2 paragraph 1 sentence 1 since you have a colon with comma seperated list, can you say exactly matching, very short... It took me a while to figure out what you were suggesting, but I think I prefer the parallelism of the current list, in which each item gives a length followed by how the residue is found. 2.2 paragraph 4 sentence 1 this sentence confused me a little..after "Undertaker also has oeprators for repositioning subtrees I am expecting a list, and I am not sure if there is a relationship between jiggling and trying to find the optimal placement... Good point. I'll rewrite into multiple sentences: {\Undertaker} also has operators for repositioning subtrees. It can either jiggle them a small amount or try to find the optimal placement for them, given the constraints and peptide bonds on the segments in the tree. There are various ways of splitting the tree into subtrees, which move larger or smaller sections of the protein. 2.3 paragraph 2 sentence 2 is comma necessary? Yes, I think so. 2.4 para 2 sent 1 Should yousay the basic cost functions can also... What you suggest is OK, but I think that I like the use of the reflexive "themselves" here to emphasize the point. 2,4 p 2 s 2 and 3 should these 2 sentences be switched? Yes, I think your order is better. 2.4 p 3 s 2 do you want to say "the number of atoms within a given radius for each residue... Yes, that order is better---what I had is a remnant of a longer sentence that was trimmed back, but not completely cleaned up. 2.4 p 6 s 1 important, basic? No, in this case I'm treating "basic score function" as a single object, and am trying to say that one is important, not that some score function is both basic and important, which is what the comma would imply. 2.4 p 6 s last This sentence last? I'm not sure what you are questioning here. I think that this final sentence is appropriate to the paragraph, and it makes a fairly good transition to the next section. 3 p 1 s last comma aftyer For the difficult targets, Yes, but after the parentheses. 3 p 3 s 2 should you say "This is not surprising, given... Yes. 3.1 p 1 s 1 what we thought were? Hmm, the sentence is too easily misinterpreted. I rewrote to "Target T0129 was the first target to be released, and so we had plenty of time to look at it and to adjust the scoring function of {\undertaker} to produce more protein-like conformations." 3.1 p2 s 2 We mentally partitioned it? OK, but "the target", since there is no obvious antecedant for "it" 3.3 p 1 s 2 can you say "Only our fold-recognition ... No, I meant "our fold-recognition technique without further help" rather than "our fold-recognition technique and no one else's". Perhaps I'll replace "alone" with "by itself" to reduce ambiguity. 3.3 p2 s 1 do you want to end sentence after assembled That is a rather long sentence, isn't it? I split it "When {\undertaker} was run with no hand-added constraints, the sheet was not assembled. To assemble it, we tried to find topologies that were consistent with our predictions that strand~1 would be an anti-parallel or mixed middle strand, ..." The second sentence is still a bit too long, but making it shorter would be a lot of work. 3.3 p2 s2 sheets, resulted ? (paragraph 3, not 2) Yes, another copy editor caught this already. 3.3 p2 s3 I dont really get this sentence. Typo? Yes, I was missing a word: "We superimposed the models and did cut-and-paste editing TO put together a model with better features, which we then reoptimized." From ScholarOneMailer@ScholarOne.com Mon Mar 3 16:42:44 2003 Date: Mon, 3 Mar 2003 19:42:41 -0500 To: karplus@soe.ucsc.edu Subject: PSFG- Manuscript Prot-00100-2003 From: proteins@jhu.edu Cc: X-SpamBouncer: 1.4 (10/07/01) X-SBNote: From Admin X-SBPass: No Freemail Filtering X-SBClass: Admin PROTEINS Structure, Function and Genetics Dear Prof. Karplus: Your manuscript "Combining local-structure, fold-recognition, and new-fold methods for protein structure prediction" has been successfully uploaded to the PROTEINS web site for submission and review. Your manuscript number is Prot-00100-2003 . Please make note of your manuscript number. You can keep track of your manuscript by logging on periodically to the PROTEINS site where the status will be displayed in your Author Center. Thank you for your interest in Proteins: Structure, Function, and Genetics. PSFG Editorial Office Johns Hopkins University Department of Biophysics Jenkins Hall B6 Charles and 34th Streets Baltimore, MD 21218-2684 Phone: 410 516 0223 Fax: 410 516 0222 From ScholarOneMailer@ScholarOne.com Mon Mar 3 16:42:43 2003 Date: Mon, 3 Mar 2003 19:42:40 -0500 To: karplus@soe.ucsc.edu Subject: PSFG- Manuscript Prot-00100-2003 From: proteins@jhu.edu Cc: X-SpamBouncer: 1.4 (10/07/01) X-SBNote: From Admin X-SBPass: No Freemail Filtering X-SBClass: Admin PROTEINS Structure, Function and Genetics Dear Author: Your manuscript "Combining local-structure, fold-recognition, and new-fold methods for protein structure prediction" has been successfully uploaded to PROTEINS. Your manuscript number is Prot-00100-2003 . Please make note of your manuscript number. Within 24 hours, your co-authors will also receive an e-mail confirming the receipt of your submission. This process will also serve to validate the e-mail addresses that you have provided. You can keep track of your manuscript by logging on periodically to the PROTEINS site where the status will be displayed in your Author Center. Thank you for your interest in Proteins: Structure, Function, and Genetics. PSFG Editorial Office Johns Hopkins University Department of Biophysics Jenkins Hall B6 Charles and 34th Streets Baltimore, MD 21218-2684 Phone: 410 516 0223 Fax: 410 516 0222 From karplus@bray.cse.ucsc.edu Mon Mar 3 16:45:22 2003 Date: Mon, 3 Mar 2003 16:45:26 -0800 From: Kevin Karplus To: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu, learithe@cats.ucsc.edu, yael@biology.ucsc.edu, jcasper@soe.ucsc.edu, rph@soe.ucsc.edu, markd@soe.ucsc.edu Subject: CASP5 paper submitted! I submitted the paper at 16:42 this afternoon. It's done (until the reviewers shred it). Thanks for all the help! Kevin From fidelis@llnl.gov Mon Feb 24 09:36:16 2003 MIME-Version: 1.0 X-Sender: e272374@popcorn.llnl.gov Date: Mon, 24 Feb 2003 09:29:51 -0800 To: Kevin Karplus From: Krzysztof Fidelis Subject: Re: CASP5 results In-Reply-To: <200302230132.h1N1WbA12189@bray.cse.ucsc.edu> Content-Type: multipart/alternative; boundary="=====================_-778314187==_.ALT" X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK --=====================_-778314187==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Kevin, We are trying to fix this. Meanwhile I have tried to contact you by phone to assess what can we do to help even before this problem is corrected. Please give me a call at 925 423 4752. Krzysztof At 05:32 PM 2/22/2003 -0800, you wrote: >I've been trying to get my CASP5 paper finished, but been stymied by >the unavailability of the graphical results. I tried clicking on >"graphical results" on >http://predictioncenter.llnl.gov/casp5/pubResultS/CASP_BROWSER/casp5-browsers.cgi >and got > Not Found > The requested URL /casp5/pubResultS/CASP_PLOTS/summary_gdt.html was > not found on this server. > > >I tried looking at the results all proteins for group 001 and got >http://predictioncenter.llnl.gov/casp5/pubResultS/CASP_BROWSER/3d-browser/3d_res.cgi > The results of the evaluation of prediction(s) > Number of selected predictions: 0 > The results are sorted by: > TARGET -> GDT_TS -> CRMSCA(ALL_ATOMS) > >But I had selected all predictions! Either the web pages don't work >with Netscape or there is something wrong with the server (or there is >something so wrong with the human interface that I can't figure out >how to use it). > >I could go into individual targets with the non-interactive pages, but >all attempts to get to any of the graphical outputs resulted in >messages like > Not Found > The requested URL > /casp5/pubResultS/CASP_BROWSER/graphs/LCS/T0184TS189_2.T0184_1.html > was not found on this server. > > >I was hoping to do some comparison between my server and my hand >method (already a difficult task on the CASP5 results pages, since >there seems to be no way to compare two groups without a lot of >flipping back and forth between pages). But if I can't even see the >results for one of the groups, I don't know how I'm going to write >about what went right and what went wrong. > >Kevin Karplus --=====================_-778314187==_.ALT Content-Type: text/html; charset="us-ascii" Kevin,

We are trying to fix this. Meanwhile I have tried to contact you by phone to assess what can we do to help even before this problem is corrected. Please give me a call at 925 423 4752.

Krzysztof



At 05:32 PM 2/22/2003 -0800, you wrote:
I've been trying to get my CASP5 paper finished, but been stymied by
the unavailability of the graphical results.  I tried clicking on
"graphical results"  on
http://predictioncenter.llnl.gov/casp5/pubResultS/CASP_BROWSER/casp5-browsers.cgi
and got
    Not Found
    The requested URL /casp5/pubResultS/CASP_PLOTS/summary_gdt.html was
    not found on this server.


I tried looking at the results all proteins for group 001 and got
http://predictioncenter.llnl.gov/casp5/pubResultS/CASP_BROWSER/3d-browser/3d_res.cgi
    The results of the evaluation of prediction(s)
    Number of selected predictions: 0
    The results are sorted by:
    TARGET -> GDT_TS -> CRMSCA(ALL_ATOMS)

But I had selected all predictions!  Either the web pages don't work
with Netscape or there is something wrong with the server (or there is
something so wrong with the human interface that I can't figure out
how to use it).

I could go into individual targets with the non-interactive pages, but
all attempts to get to any of the graphical outputs resulted in
messages like
    Not Found
    The requested URL
    /casp5/pubResultS/CASP_BROWSER/graphs/LCS/T0184TS189_2.T0184_1.html
    was not found on this server.


I was hoping to do some comparison between my server and my hand
method (already a difficult task on the CASP5 results pages, since
there seems to be no way to compare two groups without a lot of
flipping back and forth between pages).  But if I can't even see the
results for one of the groups, I don't know how I'm going to write
about what went right and what went wrong.

Kevin Karplus
--=====================_-778314187==_.ALT-- From nobody@carbns.umbi.umd.edu Wed Jan 8 08:59:43 2003 MIME-Version: 1.0 From: Announcements To: karplus@soe.ucsc.edu Reply-To: Announcements Organization: Announcements List: announce List-Archive: http://www.forcasp.org/cgi-bin/mojo/mojo.cgi?f=archive&l=announce List-ID: 20030108124811 List-Owner: List-Subscribe: http://www.forcasp.org/cgi-bin/mojo/mojo.cgi?f=s&l=announce List-Unsubscribe: http://www.forcasp.org/cgi-bin/mojo/mojo.cgi?f=u&l=announce List-URL: http://www.forcasp.org/cgi-bin/mojo/mojo.cgi?l=announce List-Software: Mojo Mail 2.7.1 Precedence: list X-Priority: 3 Subject: CASP5 special issue paper selection Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Date: Wed, 8 Jan 2003 12:48:16 -0500 (EST) X-SpamBouncer: 1.4 (10/07/01) X-SBNote: From Admin X-SBNote: FROM_DAEMON/Listserv X-SBPass: No Freemail Filtering X-SBClass: Admin Dear CASP5 predictor: As discussed briefly at the Asilomar meeting, we are hoping to select one or two papers for inclusion in the CASP special issue on the basis of novel and promising methods. The mechanism for selection will be via the CASP5 abstracts on the FORCASP website. There will be one week (January 9 - 19) during which all CASP predictors may add comments on the merit of different methods. The idea is to first generate discussion on possibly interesting methods, so that voting will be more informed and considered. Then, there will be a period of three days (January 20 - 22) in which any CASP predictor may vote on which groups should be invited to submit special issue papers. Some people may not have taken as much care in preparing their abstracts as they might have done, had this use been known in advance. To partly compensate, it is possible to extend the information in the abstract in the form of a comment. Also, links (URLs, medline IDs) can be added using the tool box. Please bear in mind that this is the first time we have tried any thing like this, and exactly how the system will behave is unknown. There could be reasons why the outcome is not satisfactory, voting needs to be repeated , or no extra papers are included in the special issue. Hopefully we will get a useful outcome, and at the very least, will know how to do things right for CASP6. The procedure for registering, commenting and voting is given below. Questions concerning the overall process should be sent to John Moult at moult@umbi.umd.edu. Questions about difficulties with passwords, login problems or lost CASP IDs should be sent to Eugene Melamud at melamud@carb.nist.gov. We will add to the FAQs on the site as questions come in, so please check there before emailing. John Moult ----------------- Registration: The first step is to create a user account. You can do this by clicking on "Your Account" link located on the top of the FORCASP webpage (www.forcasp.org). After completion of the form, you will immediately be sent an email with your password, so make sure your email address is valid. In order to have voting rights you must provide a valid CASP Predictor ID when registering. Your CASP Predictor ID is the 12 digit credit-card like number (XXXX-XXXX-XXXX) that was send to you when you registered for the CASP5 experiment. If you have multiple CASP IDs, we will accept any one of them. Commenting: Once you receive your password, you can login and start commenting. To see a list of the available abstracts click on the "CASP5 Abstracts" link in the Categories box. The abstracts are displayed in sets of 20 per page. To read a full abstract, click on the"READ MORE" link. To add a comment to an abstract, click on the "POST COMMENT" button inside the article page. Your comment will appear immediately below the article text. You can also let other people know if you like or dislike their comments by clicking on Rank Up and Rank Down links in the comment header. By ranking up the comment you increase it's total score and give the person who posted the comment more karma points, ranking down a comment will have the opposite effect. Voting: The voting form is displayed on the left an abstract text. Once voting begins, you can vote on as many abstracts as you like, but you get only one vote per abstract and that vote can not be changed. The vote scale is from 1 (poor) to 5 ( excellent). Remember that votes should be made on the novelty and potential of the methods described. If you want to see a record of all your votes, as well as a list of abstracts that you have not yet voted on, click "QUICK VOTE VIEW" located on the top of the category page. -- To unsubscribe from: Announcements, just follow this link: http://www.forcasp.org/cgi-bin/mojo/mojo.cgi?f=u&l=announce&e=karplus@soe.ucsc.edu&p=6003 Click this link, or copy and paste the address into your browser. FORCASP: http://www.forcasp.org From ScholarOneMailer@ScholarOne.com Thu Apr 3 13:14:12 2003 Date: Thu, 3 Apr 2003 16:14:04 -0500 To: karplus@soe.ucsc.edu Subject: PSFG- Manuscript Prot-00100-2003 From: proteins@jhu.edu Cc: yael@soe.ucsc.edu, jcasper@soe.ucsc.edu, learithe@soe.ucsc.edu, rachelk@soe.ucsc.edu, karplus@soe.ucsc.edu, markd@soe.ucsc.edu, rph@soe.ucsc.edu X-SpamBouncer: 1.4 (10/07/01) X-SBNote: From Admin X-SBPass: No Freemail Filtering X-SBClass: Admin PROTEINS Structure, Function and Genetics Dear Prof. Kevin Karplus: I am pleased to inform you that your manuscript has been accepted for publication in the next available issue of Proteins: Structure, Function, and Genetics. I have placed this manuscript in the "accept" cagtegory, rather than in "minor revision", to expedite publication. Please make the small changes requested before submitting the final version as described below. If you have not already done so, please forward to the Editorial office two complete copies of your manuscript, a diskette or CD with the text and figures, and the Copyright Transfer Form to the address in the signature below. Also note that the "Copyright Transfer Form" is available online at: http://prot-wiley.manuscriptcentral.com/index.html?mode=instruction. While all authors' signatures are preferred on the CT form, the senior/corresponding author's signature is required. The CT form must be returned to the Proteins Editorial Office (regular post, e-mail or fax) before the manuscript can be forwarded to Wiley Production. DELAYS IN THE RETURN OF YOUR MANUSCRIPT, DISK AND CT FORM WILL RESULT IN AN INDEFINITE DELAY IN PUBLICATION, SO PLEASE RETURN THE REQUESTED ITEMS PROMPTLY. Please pay particular attention to the note at the end of this e-mail regarding color charges. Congratulations on submitting such an excellent study. Sincerely, Ed Lattman Editor-in-Chief PSFG Editorial Office Johns Hopkins University Department of Biophysics Jenkins Hall B6 Charles and 34th Streets Baltimore, MD 21218-2684 Phone: 410 516 0223 Fax: 410 516 0222 NOTE: Color Reproduction Charges. Please note that Proteins provides you one published page of color free of charge. You will be charged for any additional pages of color at $500 per page. The publisher will make every attempt to fit the most number of color figures on a page to incur minimal costs to authors. You will be faxed a color charge form within three weeks after the receipt of your manuscript and diskette. Failure to return the completed form to the production editor promptly will delay publication of your article. Editorial Manager's Comments to Author: The authors need to address the number of small points raised by the both reviewers to improve the clarity of the manuscript. Reviewers' Comments to Author: Reviewer 1 Comments: This manuscript is reasonably succinct and well written. In the interest of meeting the space requirements, however, the authors have at a few points been too brief. While the manuscript in its current form is acceptable for publication, the authors might want to address the issues below to achieve greater clarity and readability. Define the adjective “multi-track” used to describe the type of HMM used. I infer that “fragment insertion” means “fragment substitution”, but I am not positive. If it does, then the authors would be better off using “substitution”, because this more explicitly describes the operation – a pre-existing segment is removed and a new one inserted. “Insertion” implies that nothing was present initially. The description on page 3 of the representation of protein structure as a tree of segments is not at all clear. Part of the problem is the description “… tertiary edges, indicate which pairs of atoms are though of as holind the segments together.” Are these hypothetical covalent bonds, because of missing residues between otherwise connected residues? Or are these hypothetical non-covalent bonds, as in tertiary contacts? In addition, the function served by this tree is not at all clear. What good does it do? The description of the individual CASP models could be shortened in the interest of making the methodology more clear. These chatty descriptions are filled with anecdotal snippets that don’t contribute to a better picture of what was actually done. Reviewer 2 Comments: This paper describes SAM-T02 and undertaker as applied to CASP5 targets. My summary statement is that it should be written more carefully, so that the reader can better follow the logic behind the methods and (in principle at least) reconstruct the algorithms. At least one figure should be added to aid the reader in understanding the big picture (sec 2.3 and parts of 2.1) These are minor changes, but I think they will improve readability and make this special issue more useful to people who may be thinking of participating in CASP6! Specific comments follow: p.1 "Our group was selected to speak..." This is not a scientific approach to validation, although it may be the CASP way. Rephrase it. Figure 1. The dot is barely visible. Why not use a bold arrow? p.3. "The fragfinder method was developed during the summer..." This sounds apologetic. There are many Latex typos that should be fixed. (e.g. look at the word undertaker in the PDF) p.3 "torsion angles for the NH3 and OH groups would need to be set." No. Think about it. These bonds rotate freely. You can simply calculate the H positions. p.3 "To solve this problem... subtrees rigidly transformed..." I think this paragraph is critical to understanding the novel aspects of Undertaker. How are the subtrees rigidly transformed? Torsion space fragment insertion? Rigidbody energy minimization of MC search? (If this is discussed elsewhere in the paper, why not say so.) A figure would be nice here. The paper should include a step-by-step description of the method, including the order of operations and the decisions that are made along the way. For example, when and how do you decide to do an "alignment insertion"? (sec 2.2) The current text is like a collection of ideas, with no clear overall scheme. Section 2.3 clarifies the overall scheme somewhat, but this should appear before secs 2.1 and 2.2 p.4 "our cost function does not yet include a H-bonding term" This is shocking if what you are doing is simulation, but not so shocking if what you are doing is fold recognition, since fragments, especially helix, have the h-bonds built in. Are other cost functions capturing the H-bonds? p.5 Sec 3. Everyone focuses on the successful cases. Why not focus on a conspicuous failure? Here is where we can learn the most. p.5 "We did well" is not a useful statement . Is there a class of folds for which the method succeeds? Be specific. p.6 The story about T0139 is interesting but should be removed. I don't think it is of interest to know how published pictures can help us predict structure. Michael Rossman figured out how to do this in the 70's. From rachelk@grunt.cse.ucsc.edu Tue Apr 29 17:27:26 2003 MIME-Version: 1.0 From: Rachel Karchin Content-Type: text/plain; charset=us-ascii Date: Tue, 29 Apr 2003 17:27:25 -0700 To: karplus@soe.ucsc.edu Subject: revising the casp paper X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK How do you want to handle our "multiple revisors" situation? casp5.tex is currently writable only by you. After I'm done with my changes, I can put a revised new version in the directory, but then you'll have to handle merging my changes with any that you've made. -- rk From karplus@bray.cse.ucsc.edu Tue Apr 29 20:36:45 2003 Date: Tue, 29 Apr 2003 20:36:45 -0700 From: Kevin Karplus To: rachelk@soe.ucsc.edu CC: karplus@soe.ucsc.edu In-reply-to: <16047.6253.177661.283882@grunt.cse.ucsc.edu> (message from Rachel Karchin on Tue, 29 Apr 2003 17:27:25 -0700) Subject: Re: revising the casp paper I created a new directory casp5-prosfg-final with a writable copy of the paper. Go ahead and edit it in place. I'll let you know when I'm ready to make my changes. From karplus@bray.cse.ucsc.edu Fri May 9 09:50:35 2003 Date: Fri, 9 May 2003 09:50:36 -0700 From: Kevin Karplus To: learithe@soe.ucsc.edu CC: karplus@soe.ucsc.edu Subject: picture for CASP5 paper X-Spam-Status: No, hits=-102.5 required=3.0 tests=AWL,USER_IN_WHITELIST version=2.53 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.53 (1.174.2.15-2003-03-30-exp) Referee 2 for the paper CASP5 commented At least one figure should be added to aid the reader in understanding the big picture (sec 2.3 and parts of 2.1). I was wondering if you could help out with that. I have a small figure that I've used for some papers /cse/faculty/karplus/pcp/protein-structure/germany02/sam-undertaker/figures/methods.eps (and .xfig) but it does not include fragfinder and undertaker. Do you think that you could modify it or create a new, better-looking picture of the overall process? Kevin From karplus@bray.cse.ucsc.edu Mon May 12 10:27:58 2003 Date: Mon, 12 May 2003 10:27:59 -0700 From: Kevin Karplus To: learithe@soe.ucsc.edu CC: karplus@soe.ucsc.edu Subject: low-quality sketch of workflow for CASP5 paper X-Spam-Status: No, hits=-102.3 required=3.0 tests=AWL,USER_IN_WHITELIST version=2.53 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.53 (1.174.2.15-2003-03-30-exp) I stuck a low-quality sketch of the workflow for CASP5 predictions. Feel free to move thinsg around to make it look better. I would like a generally top-to-bottom, left-to-right flow (so the final ouput should be further right than I've drawn it). I'd like the boxes to correspond to files (or sets of files) and the arrows to be labeled with program names. Kevin From learithe@croak.cse.ucsc.edu Fri May 9 18:51:00 2003 MIME-Version: 1.0 Date: Fri, 9 May 2003 18:50:59 -0700 (PDT) From: Jenny Draper To: Kevin Karplus Subject: Re: picture for CASP5 paper In-Reply-To: <200305100004.h4A04YX17492@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-118.2 required=3.0 tests=AWL,EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, REPLY_WITH_QUOTES,USER_AGENT_PINE,USER_IN_WHITELIST autolearn=ham version=2.53 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.53 (1.174.2.15-2003-03-30-exp) Sounds good. -Jenny On Fri, 9 May 2003, Kevin Karplus wrote: > I'll put some sort of sketch together this weekend, and give it to you > on Monday. > From karplus@bray.cse.ucsc.edu Sat May 24 15:13:31 2003 Date: Sat, 24 May 2003 15:13:34 -0700 From: Kevin Karplus To: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu, learithe@soe.ucsc.edu, jcasper@soe.ucsc.edu, yael@soe.ucsc.edu, markd@soe.ucsc.edu, rph@soe.ucsc.edu Subject: CASP5 paper revised X-Spam-Status: No, hits=-101.7 required=3.0 tests=AWL,USER_IN_WHITELIST version=2.53 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.53 (1.174.2.15-2003-03-30-exp) I think I've finished the CASP5 revisions. The paper is in /projects/compbio/papers/protein-structure/casp5/casp5-prosfg-final/casp5.tex (also .dvi and .ps , but I couldn't get either pdflatex or distill to work to produce a pdf file) Hmm---ghostview seems to have problems with the file also. It looks like the problems are coming from the EPS file that Jenny gave me for the picture in Figure 2. Jenny, could you look into the problem---see if you can include the SamWorld.eps file in other LaTeX files, ... If you could debug this, it would be a big help. Other than the problem with the eps file not working, I think we're done. I'd appreciate it if people could check the paper for any last-minute changes, so we can send it out this week. The referees' comments and my responses are in /projects/compbio/papers/protein-structure/casp5/casp5-prosfg-final/responses-to-referees From jcasper@baa.cse.ucsc.edu Sat May 24 15:43:22 2003 MIME-Version: 1.0 Date: Sat, 24 May 2003 15:43:01 -0700 (PDT) From: Jonathan Casper To: Kevin Karplus cc: rachelk@soe.ucsc.edu, , , , , Subject: Re: CASP5 paper revised In-Reply-To: <200305242213.h4OMDYF00844@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-UCSC-CATS-MailScanner: Found to be clean X-UCSC-CATS-MailScanner-SpamCheck: X-Spam-Status: No, hits=-116.1 required=3.0 tests=EMAIL_ATTRIBUTION,QUOTED_EMAIL_TEXT,QUOTE_TWICE_1, USER_AGENT_PINE,USER_IN_WHITELIST autolearn=ham version=2.53 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.53 (1.174.2.15-2003-03-30-exp) Kevin, I'm going to try something with SamWorld.eps - I'm changing the CropBox and the HiResBoundingBox values a bit. I'll keep a backup in SamWorld.ps.bak. Let me know if this fixes things. -Jonathan On Sat, 24 May 2003, Kevin Karplus wrote: > > I think I've finished the CASP5 revisions. The paper is in > /projects/compbio/papers/protein-structure/casp5/casp5-prosfg-final/casp5.tex > (also .dvi and .ps , but I couldn't get either pdflatex or distill to > work to produce a pdf file) > > Hmm---ghostview seems to have problems with the file also. It looks > like the problems are coming from the EPS file that Jenny gave me for > the picture in Figure 2. > > Jenny, could you look into the problem---see if you can include the > SamWorld.eps file in other LaTeX files, ... If you could debug this, > it would be a big help. > > Other than the problem with the eps file not working, I think we're done. > I'd appreciate it if people could check the paper for any last-minute > changes, so we can send it out this week. > > The referees' comments and my responses are in > /projects/compbio/papers/protein-structure/casp5/casp5-prosfg-final/responses-to-referees > From jcasper@baa.cse.ucsc.edu Sat May 24 15:44:51 2003 MIME-Version: 1.0 Date: Sat, 24 May 2003 15:44:34 -0700 (PDT) From: Jonathan Casper To: Kevin Karplus Subject: Re: CASP5 paper revised In-Reply-To: <200305242213.h4OMDYF00844@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-UCSC-CATS-MailScanner: Found to be clean X-UCSC-CATS-MailScanner-SpamCheck: X-Spam-Status: No, hits=-110.9 required=3.0 tests=AWL,USER_AGENT_PINE,USER_IN_WHITELIST autolearn=ham version=2.53 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.53 (1.174.2.15-2003-03-30-exp) Okay, the changes are made, and the backup file is SamWorld.eps.bak. Try re-building the paper. -Jonathan From karplus@bray.cse.ucsc.edu Sat May 24 21:06:45 2003 Date: Sat, 24 May 2003 21:06:46 -0700 From: Kevin Karplus To: jcasper@soe.ucsc.edu CC: karplus@soe.ucsc.edu, learithe@soe.ucsc.edu In-reply-to: (message from Jonathan Casper on Sat, 24 May 2003 15:44:34 -0700 (PDT)) Subject: Re: CASP5 paper revised X-Spam-Status: No, hits=-101.7 required=3.0 tests=AWL,USER_IN_WHITELIST version=2.53 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.53 (1.174.2.15-2003-03-30-exp) Jonathan, I'm still getting the error messages %%[ Error: undefined; OffendingCommand: II* ]%% %%[ Flushing: rest of job (to end-of-file) will be ignored ]%% %%[ Warning: PostScript error. No PDF file produced. ] %% when I try to run distill (on apache). The II* command that is causing the problem appears after the %A19_PrivateDataEnd near the end of the postscript file. Kevin From karplus@bray.cse.ucsc.edu Wed May 28 10:13:29 2003 Date: Wed, 28 May 2003 10:13:28 -0700 From: Kevin Karplus To: karplus@soe.ucsc.edu, rachelk@soe.ucsc.edu, learithe@soe.ucsc.edu, jcasper@soe.ucsc.edu, yael@soe.ucsc.edu, markd@soe.ucsc.edu, rph@soe.ucsc.edu Subject: casp5 paper fixed X-Spam-Status: No, hits=-100.3 required=3.0 tests=AWL,USER_IN_WHITELIST version=2.53 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.53 (1.174.2.15-2003-03-30-exp) I fixed the problem with SamWorld.eps by deleting everything after PrivateDataEnd. I suspect that the problem may have been a poor copy (past end of file) from the machine that Jenny created the image on. I would like to send this paper off by tomorrow if possible. Please at least look through my responses to the referees and send me comments on them. (Even a null-content reply to let me know that you aren't going to comment would be useful.) From yael@darwin.UCSC.EDU Wed May 28 10:54:06 2003 MIME-Version: 1.0 X-Authentication-Warning: darwin.UCSC.EDU: yael owned process doing -bs Date: Wed, 28 May 2003 10:50:56 -0700 (PDT) From: yael@biology.ucsc.edu To: Kevin Karplus Subject: Re: casp5 paper fixed In-Reply-To: <200305281713.h4SHDSc12041@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-116.5 required=3.0 tests=EMAIL_ATTRIBUTION,NO_REAL_NAME,QUOTED_EMAIL_TEXT, QUOTE_TWICE_1,USER_AGENT_PINE,USER_IN_WHITELIST, X_AUTH_WARNING autolearn=ham version=2.53 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.53 (1.174.2.15-2003-03-30-exp) Hi, I was not available during the weekend and I have a deadline to send out a proposal this week but I will look through the comments later today and let you know if I have any remarks. Yael Yael Mandel-Gutfreund MCD Biology University of California, Santa Cruz Phone : 831-459-2612 /459-4917 Fax : 831-459-3139 e-mail : yael@darwin.ucsc.edu On Wed, 28 May 2003, Kevin Karplus wrote: > > I fixed the problem with SamWorld.eps by deleting everything after > PrivateDataEnd. I suspect that the problem may have been a poor copy > (past end of file) from the machine that Jenny created the image on. > > I would like to send this paper off by tomorrow if possible. > Please at least look through my responses to the referees and send me > comments on them. (Even a null-content reply to let me know that you > aren't going to comment would be useful.) > > From yael@darwin.UCSC.EDU Thu May 29 01:07:46 2003 MIME-Version: 1.0 X-Authentication-Warning: darwin.UCSC.EDU: yael owned process doing -bs Date: Thu, 29 May 2003 01:04:37 -0700 (PDT) From: yael@biology.ucsc.edu To: Kevin Karplus Subject: Re: CASP5 paper revised In-Reply-To: <200305242213.h4OMDYF00844@bray.cse.ucsc.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-116.5 required=3.0 tests=EMAIL_ATTRIBUTION,NO_REAL_NAME,QUOTED_EMAIL_TEXT, QUOTE_TWICE_1,USER_AGENT_PINE,USER_IN_WHITELIST, X_AUTH_WARNING autolearn=ham version=2.53 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.53 (1.174.2.15-2003-03-30-exp) HI Kevin,Sorry I just got to read the response to the referee now. Overall they look ok though I don't feel that the second referees comments were fully answered, but since they are quite annoying I think you did the best you could. Small comments: The last answer to ref 1 : I would omit the first sentence. In this case I actually agree with the referee but since you don't I would just say : "we feel that..." ref 2 comment page 4: I do not think the answer is satisfying, but I presume nothing would ref 2 comment to page 5 sec 3: To be consistent you should say "we disagree.." ref 2 to p.5 we did well I don't think it is satisfying to say that we did not do testing because we didn't want to spent the effort. If I would be him I would expect that they should do some evaluation... but maybe in a casp paper it is ok Yael Yael Mandel-Gutfreund MCD Biology University of California, Santa Cruz Phone : 831-459-2612 /459-4917 Fax : 831-459-3139 e-mail : yael@darwin.ucsc.edu On Sat, 24 May 2003, Kevin Karplus wrote: > > I think I've finished the CASP5 revisions. The paper is in > /projects/compbio/papers/protein-structure/casp5/casp5-prosfg-final/casp5.tex > (also .dvi and .ps , but I couldn't get either pdflatex or distill to > work to produce a pdf file) > > Hmm---ghostview seems to have problems with the file also. It looks > like the problems are coming from the EPS file that Jenny gave me for > the picture in Figure 2. > > Jenny, could you look into the problem---see if you can include the > SamWorld.eps file in other LaTeX files, ... If you could debug this, > it would be a big help. > > Other than the problem with the eps file not working, I think we're done. > I'd appreciate it if people could check the paper for any last-minute > changes, so we can send it out this week. > > The referees' comments and my responses are in > /projects/compbio/papers/protein-structure/casp5/casp5-prosfg-final/responses-to-referees > > From rph@cse.ucsc.edu Wed May 28 15:42:38 2003 MIME-Version: 1.0 From: "rph" To: "Kevin Karplus" Subject: RE: casp5 paper fixed Date: Wed, 28 May 2003 15:42:38 -0700 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal In-Reply-To: <200305281713.h4SHDSc12041@bray.cse.ucsc.edu> Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4910.0300 X-Spam-Status: No, hits=-103.1 required=3.0 tests=AWL,QUOTED_EMAIL_TEXT,USER_IN_WHITELIST autolearn=ham version=2.53 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.53 (1.174.2.15-2003-03-30-exp) last sentence on page 2 is hard to parse 'The automatic server...' p6: cite or www for robetta '(T0139)' should be (T0130) refs inconsistent on first names, espc ref 5. Looks great! Well done again! Richard > -----Original Message----- > From: Kevin Karplus [mailto:karplus@soe.ucsc.edu] > Sent: Wednesday, May 28, 2003 10:13 AM > To: karplus@soe.ucsc.edu; rachelk@soe.ucsc.edu; > learithe@soe.ucsc.edu; > jcasper@soe.ucsc.edu; yael@soe.ucsc.edu; markd@soe.ucsc.edu; > rph@soe.ucsc.edu > Subject: casp5 paper fixed > > > > I fixed the problem with SamWorld.eps by deleting everything after > PrivateDataEnd. I suspect that the problem may have > been a poor copy > (past end of file) from the machine that Jenny created > the image on. > > I would like to send this paper off by tomorrow if possible. > Please at least look through my responses to the referees > and send me > comments on them. (Even a null-content reply to let me > know that you > aren't going to comment would be useful.) > From rachelk@grunt.cse.ucsc.edu Wed May 28 12:29:37 2003 MIME-Version: 1.0 From: Rachel Karchin Content-Type: text/plain; charset=us-ascii Date: Wed, 28 May 2003 12:29:36 -0700 To: Kevin Karplus Subject: Re: casp5 paper fixed In-Reply-To: <200305281713.h4SHDSc12041@bray.cse.ucsc.edu> X-Spam-Status: No, hits=-115.5 required=3.0 tests=AWL,EMAIL_ATTRIBUTION,QUOTED_EMAIL_TEXT,USER_AGENT_VM, USER_IN_WHITELIST autolearn=ham version=2.53 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.53 (1.174.2.15-2003-03-30-exp) Sorry for the delayed response. I was in San Francisco yesterday at the Sali lab, spent the night in Palo Alto, and am finally back to work in Santa Cruz as of Wednesday morning! btw -- I have accepted Andrej's offer and will be starting as a postdoc in his lab on August 1. Biggest problem: Figure 2 is so small as to be unreadable. Also the directed arrows are labeled with program names that are not identified in the caption or the text: w0.5, hmmscore, predict-2nd one very small edit: Section 2.4, third paragraph shouldn't have a comma after "counts" -- rk Kevin Karplus writes: > > I fixed the problem with SamWorld.eps by deleting everything after > PrivateDataEnd. I suspect that the problem may have been a poor copy > (past end of file) from the machine that Jenny created the image on. > > I would like to send this paper off by tomorrow if possible. > Please at least look through my responses to the referees and send me > comments on them. (Even a null-content reply to let me know that you > aren't going to comment would be useful.) From karplus@bray.cse.ucsc.edu Thu May 29 17:19:10 2003 Date: Thu, 29 May 2003 17:19:16 -0700 From: Kevin Karplus To: karplus@soe.ucsc.edu Subject: PSFG- Manuscript Prot-00100-2003 X-Spam-Status: No, hits=-106.2 required=3.0 tests=AWL,BAYES_01,USER_IN_WHITELIST version=2.53 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.53 (1.174.2.15-2003-03-30-exp) Copy of mail To: proteins@jhu.edu I have finished the corrections to my CASP5 paper PSFG- Manuscript Prot-00100-2003 The final copy is available in LaTeX, postscript, and PDF formats at http://www.soe.ucsc.edu/~karplus/papers/casp5/ I will send 2 copies and the signed copyright form by US mail, but I won't send a diskette---you can get the files off the web quicker and more reliably. Here are our responses to the referree's comments: PSFG- Manuscript Prot-00100-2003 PROTEINS Structure, Function and Genetics Responses to referees: Reviewer 1 Comments: This manuscript is reasonably succinct and well written. In the interest of meeting the space requirements, however, the authors have at a few points been too brief. While the manuscript in its current form is acceptable for publication, the authors might want to address the issues below to achieve greater clarity and readability. Define the adjective "multi-track" used to describe the type of HMM used. OK, we've attempeted a brief explanation of "multi-track HMMs", added our standard picture, and added citations to more detailed descriptions. I infer that "fragment insertion" means "fragment substitution", but I am not positive. If it does, then the authors would be better off using "substitution", because this more explicitly describes the operation – a pre-existing segment is removed and a new one inserted. "Insertion" implies that nothing was present initially. We had copied Baker's group in calling the operation "fragment insertion", but like the names "fragment substitution" or "fragment replacement" better. Thanks for the suggestion---we have adopted "fragment replacement". The description on page 3 of the representation of protein structure as a tree of segments is not at all clear. Part of the problem is the description "... tertiary edges, indicate which pairs of atoms are though of as holind the segments together." Are these hypothetical covalent bonds, because of missing residues between otherwise connected residues? Or are these hypothetical non-covalent bonds, as in tertiary contacts? In addition, the function served by this tree is not at all clear. What good does it do? We have tried to clarify this without taking up too much space. We could add a lot more, but the details seemed outside the scope of the CASP5 paper. The description of the individual CASP models could be shortened in the interest of making the methodology more clear. These chatty descriptions are filled with anecdotal snippets that don't contribute to a better picture of what was actually done. We feel that the "anecdotal snippets" increase the readability of the paper and make it clearer where our techniques were more ad hoc rather than algorithmic. Reviewer 2 Comments: This paper describes SAM-T02 and undertaker as applied to CASP5 targets. My summary statement is that it should be written more carefully, so that the reader can better follow the logic behind the methods and (in principle at least) reconstruct the algorithms. While detailed descriptions that would allow the reader to reconstruct the algorithms are very nice in theory, there is hardly room in this paper for that level of detail---especially as several of the new-fold "successes" relied on human intuition and luck in assembling beta sheets, rather than a duplicatable algorithm. At least one figure should be added to aid the reader in understanding the big picture (sec 2.3 and parts of 2.1) These are minor changes, but I think they will improve readability and make this special issue more useful to people who may be thinking of participating in CASP6! We have added such a figure---I hope it is helpful. Specific comments follow: p.1 "Our group was selected to speak..." This is not a scientific approach to validation, although it may be the CASP way. Rephrase it. We've rephrased to "According to the {\casp5} assesors, our group had good results in the new-fold category and the analogous fold-recognition category, so the new fragment-packing program, {\undertaker}, will be the main focus of this paper." This may not be much better, but does explain why we are not talking much about the fold-recognition methods. Figure 1. The dot is barely visible. Why not use a bold arrow? Good suggestion. We've adopted it. p.3. "The fragfinder method was developed during the summer..." This sounds apologetic. Well, it was apologetic. We've changed to "Although we have not yet optimized the {\fragfinder} method nor done extensive testing, ..." There are many Latex typos that should be fixed. (e.g. look at the word undertaker in the PDF) Fixed---This was a typo: having \ss instead of \sc in the macros defining \undertaker and \fragfinder. p.3 "torsion angles for the NH3 and OH groups would need to be set." No. Think about it. These bonds rotate freely. You can simply calculate the H positions. Calculating the H positions IS setting the torsion angles. If the torsion angle is computed within the energy function, then explicit hydrogens aren't being used---only implicit ones. We are currently working on a hydrogen-bond scoring function that uses only implicit hydrogens. We expect it to work fairly well for single hydrogen bonds, but it may have trouble with multiple hydrogen bonds involving the same donor or acceptor (of course, these can be problematic even with explicit hydrogens, since the multiple H-bonds are not simply additive). In any case, more details of this current and future work seem a bit out of place in the CASP5 paper. We've added only one sentence to clarify the paragraph: "We could optimize the torsion angles after determining that an H-bond was desired, but this does not seem to offer much advantage over the current implicit hydrogens." p.3 "To solve this problem... subtrees rigidly transformed..." I think this paragraph is critical to understanding the novel aspects of Undertaker. How are the subtrees rigidly transformed? Torsion space fragment insertion? Rigidbody energy minimization of MC search? (If this is discussed elsewhere in the paper, why not say so.) A figure would be nice here. The conformation-change operators are described in the next section of the paper. The paragraphs about the subtrees have been rewritten based on referee 1's comments and a forward reference to the section on conformation-change operators added. The paper should include a step-by-step description of the method, including the order of operations and the decisions that are made along the way. For example, when and how do you decide to do an "alignment insertion"? (sec 2.2) The current text is like a collection of ideas, with no clear overall scheme. Section 2.3 clarifies the overall scheme somewhat, but this should appear before secs 2.1 and 2.2 We have added the following sentence just before Section 2.1: "Undertaker used the alignments to get an initial conformation, then applied many rounds of a genetic algorithm with randomly applied conformation-change operations to minimize a cost function." p.4 "our cost function does not yet include a H-bonding term" This is shocking if what you are doing is simulation, but not so shocking if what you are doing is fold recognition, since fragments, especially helix, have the h-bonds built in. Are other cost functions capturing the H-bonds? The H-bonds are not captured in any of the cost functions except manually-added constraints. For close fold recognition targets, the compactness of the right structure usually held it together in the subsequent optimization of the cost, but for more distant folds and new folds, the beta sheets often came apart during optimization, even if they were present in the fold-recognition alignment. We've added an extra sentence to clarify this. p.5 Sec 3. Everyone focuses on the successful cases. Why not focus on a conspicuous failure? Here is where we can learn the most. We disagree---there is little to learn from the failures in ab-initio prediction, since failure is practically ubiquitous and the processes are all fairly complex with many places where failure could have come from. If we can figure out why something works (even poorly), we can try to extend it to more cases. Once we have something that works with some regularity, then analyzing why it fails in some cases can be productive. For fold recognition, for example, it is useful to look at the failures, since there are a number of successes and we can try to find some differences between the successful and unsuccessful cases. For the new-fold predictions, we're still so far from this that analyzing the failure is like shovelling mounds of garbage to try to find a diamond that probably isn't there anyway. p.5 "We did well" is not a useful statement . Is there a class of folds for which the method succeeds? Be specific. If we knew when the method would succeed, we'd say so. If you can figure it out from the small number of examples in the CASP5 experiment, please tell us. We haven't done extensive testing yet, because we want to fix some of the obvious flaws in the cost function and conformation generation before investing enormous resources in testing. p.6 The story about T0139 is interesting but should be removed. I don't think it is of interest to know how published pictures can help us predict structure. Michael Rossman figured out how to do this in the 70's. While it is certainly true that figuring out a structure from a picture is neither new nor surprising, the key points were that only 40 noisy distance constraints were extracted from the picture, and that our conformation-generation process got trapped in a solution with the wrong chirality for the bundle. We feel that these points justify the 2 paragraphs we included about T0139. From proteins@jhu.edu Fri May 30 06:27:56 2003 MIME-Version: 1.0 Date: Fri, 30 May 2003 09:28:07 -0400 From: Starlene Murray Subject: RE: PSFG- Manuscript Prot-00100-2003 In-reply-to: <200305300010.h4U0Aux05631@bray.cse.ucsc.edu> To: "'Kevin Karplus'" X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Content-type: text/plain; charset=us-ascii Importance: Normal X-Priority: 3 (Normal) X-MSMail-priority: Normal X-Spam-Status: No, hits=-12.9 required=3.0 tests=BAYES_01,ORIGINAL_MESSAGE autolearn=ham version=2.53 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.53 (1.174.2.15-2003-03-30-exp) Dear Dr. Karplus, Hi. It's okay to fax the Copyright Transfer form. Thanks. Starlene Murray, Editorial Coordinator Proteins Editorial Office Dept. of Biophysics, Jenkins Hall B6 Johns Hopkins University Charles & 34th Streets Baltimore, Maryland 21218-2684 Phone: (410) 516-0223 Fax: (410) 516-0222 e-mail: proteins@jhu.edu -----Original Message----- From: Kevin Karplus [mailto:karplus@soe.ucsc.edu] Sent: Thursday, May 29, 2003 8:11 PM To: psf5@jhem.jhu.edu Subject: PSFG- Manuscript Prot-00100-2003 I have finished the corrections to my CASP5 paper PSFG- Manuscript Prot-00100-2003 The final copy is available in LaTeX, postscript, and PDF formats at http://www.soe.ucsc.edu/~karplus/papers/casp5/ I will send 2 copies and the signed copyright form by US mail, but I won't send a diskette---you can get the files off the web quicker and more reliably. Here are our responses to the referree's comments: PSFG- Manuscript Prot-00100-2003 PROTEINS Structure, Function and Genetics Responses to referees: Reviewer 1 Comments: This manuscript is reasonably succinct and well written. In the interest of meeting the space requirements, however, the authors have at a few points been too brief. While the manuscript in its current form is acceptable for publication, the authors might want to address the issues below to achieve greater clarity and readability. Define the adjective "multi-track" used to describe the type of HMM used. OK, we've attempeted a brief explanation of "multi-track HMMs", added our standard picture, and added citations to more detailed descriptions. I infer that "fragment insertion" means "fragment substitution", but I am not positive. If it does, then the authors would be better off using "substitution", because this more explicitly describes the operation - a pre-existing segment is removed and a new one inserted. "Insertion" implies that nothing was present initially. We had copied Baker's group in calling the operation "fragment insertion", but like the names "fragment substitution" or "fragment replacement" better. Thanks for the suggestion---we have adopted "fragment replacement". The description on page 3 of the representation of protein structure as a tree of segments is not at all clear. Part of the problem is the description "... tertiary edges, indicate which pairs of atoms are though of as holind the segments together." Are these hypothetical covalent bonds, because of missing residues between otherwise connected residues? Or are these hypothetical non-covalent bonds, as in tertiary contacts? In addition, the function served by this tree is not at all clear. What good does it do? We have tried to clarify this without taking up too much space. We could add a lot more, but the details seemed outside the scope of the CASP5 paper. The description of the individual CASP models could be shortened in the interest of making the methodology more clear. These chatty descriptions are filled with anecdotal snippets that don't contribute to a better picture of what was actually done. We feel that the "anecdotal snippets" increase the readability of the paper and make it clearer where our techniques were more ad hoc rather than algorithmic. Reviewer 2 Comments: This paper describes SAM-T02 and undertaker as applied to CASP5 targets. My summary statement is that it should be written more carefully, so that the reader can better follow the logic behind the methods and (in principle at least) reconstruct the algorithms. While detailed descriptions that would allow the reader to reconstruct the algorithms are very nice in theory, there is hardly room in this paper for that level of detail---especially as several of the new-fold "successes" relied on human intuition and luck in assembling beta sheets, rather than a duplicatable algorithm. At least one figure should be added to aid the reader in understanding the big picture (sec 2.3 and parts of 2.1) These are minor changes, but I think they will improve readability and make this special issue more useful to people who may be thinking of participating in CASP6! We have added such a figure---I hope it is helpful. Specific comments follow: p.1 "Our group was selected to speak..." This is not a scientific approach to validation, although it may be the CASP way. Rephrase it. We've rephrased to "According to the {\casp5} assesors, our group had good results in the new-fold category and the analogous fold-recognition category, so the new fragment-packing program, {\undertaker}, will be the main focus of this paper." This may not be much better, but does explain why we are not talking much about the fold-recognition methods. Figure 1. The dot is barely visible. Why not use a bold arrow? Good suggestion. We've adopted it. p.3. "The fragfinder method was developed during the summer..." This sounds apologetic. Well, it was apologetic. We've changed to "Although we have not yet optimized the {\fragfinder} method nor done extensive testing, ..." There are many Latex typos that should be fixed. (e.g. look at the word undertaker in the PDF) Fixed---This was a typo: having \ss instead of \sc in the macros defining \undertaker and \fragfinder. p.3 "torsion angles for the NH3 and OH groups would need to be set." No. Think about it. These bonds rotate freely. You can simply calculate the H positions. Calculating the H positions IS setting the torsion angles. If the torsion angle is computed within the energy function, then explicit hydrogens aren't being used---only implicit ones. We are currently working on a hydrogen-bond scoring function that uses only implicit hydrogens. We expect it to work fairly well for single hydrogen bonds, but it may have trouble with multiple hydrogen bonds involving the same donor or acceptor (of course, these can be problematic even with explicit hydrogens, since the multiple H-bonds are not simply additive). In any case, more details of this current and future work seem a bit out of place in the CASP5 paper. We've added only one sentence to clarify the paragraph: "We could optimize the torsion angles after determining that an H-bond was desired, but this does not seem to offer much advantage over the current implicit hydrogens." p.3 "To solve this problem... subtrees rigidly transformed..." I think this paragraph is critical to understanding the novel aspects of Undertaker. How are the subtrees rigidly transformed? Torsion space fragment insertion? Rigidbody energy minimization of MC search? (If this is discussed elsewhere in the paper, why not say so.) A figure would be nice here. The conformation-change operators are described in the next section of the paper. The paragraphs about the subtrees have been rewritten based on referee 1's comments and a forward reference to the section on conformation-change operators added. The paper should include a step-by-step description of the method, including the order of operations and the decisions that are made along the way. For example, when and how do you decide to do an "alignment insertion"? (sec 2.2) The current text is like a collection of ideas, with no clear overall scheme. Section 2.3 clarifies the overall scheme somewhat, but this should appear before secs 2.1 and 2.2 We have added the following sentence just before Section 2.1: "Undertaker used the alignments to get an initial conformation, then applied many rounds of a genetic algorithm with randomly applied conformation-change operations to minimize a cost function." p.4 "our cost function does not yet include a H-bonding term" This is shocking if what you are doing is simulation, but not so shocking if what you are doing is fold recognition, since fragments, especially helix, have the h-bonds built in. Are other cost functions capturing the H-bonds? The H-bonds are not captured in any of the cost functions except manually-added constraints. For close fold recognition targets, the compactness of the right structure usually held it together in the subsequent optimization of the cost, but for more distant folds and new folds, the beta sheets often came apart during optimization, even if they were present in the fold-recognition alignment. We've added an extra sentence to clarify this. p.5 Sec 3. Everyone focuses on the successful cases. Why not focus on a conspicuous failure? Here is where we can learn the most. We disagree---there is little to learn from the failures in ab-initio prediction, since failure is practically ubiquitous and the processes are all fairly complex with many places where failure could have come from. If we can figure out why something works (even poorly), we can try to extend it to more cases. Once we have something that works with some regularity, then analyzing why it fails in some cases can be productive. For fold recognition, for example, it is useful to look at the failures, since there are a number of successes and we can try to find some differences between the successful and unsuccessful cases. For the new-fold predictions, we're still so far from this that analyzing the failure is like shovelling mounds of garbage to try to find a diamond that probably isn't there anyway. p.5 "We did well" is not a useful statement . Is there a class of folds for which the method succeeds? Be specific. If we knew when the method would succeed, we'd say so. If you can figure it out from the small number of examples in the CASP5 experiment, please tell us. We haven't done extensive testing yet, because we want to fix some of the obvious flaws in the cost function and conformation generation before investing enormous resources in testing. p.6 The story about T0139 is interesting but should be removed. I don't think it is of interest to know how published pictures can help us predict structure. Michael Rossman figured out how to do this in the 70's. While it is certainly true that figuring out a structure from a picture is neither new nor surprising, the key points were that only 40 noisy distance constraints were extracted from the picture, and that our conformation-generation process got trapped in a solution with the wrong chirality for the bundle. We feel that these points justify the 2 paragraphs we included about T0139.