From mailer@bialko.llnl.gov Wed Aug 7 14:07:18 2002 Date: Wed, 7 Aug 2002 14:07:13 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu X-SpamBouncer: 1.4 (10/07/01) X-SBNote: From Admin X-SBNote: FROM_DAEMON/Listserv X-SBPass: No Freemail Filtering X-SBClass: Admin # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Wed Aug 7 13:40:06 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_524110_19613 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0170SS389_1 Current information on models submitted in prediction T0170SS389 MODEL_INDEX PIN CODE DATE E-mail T0170SS389_1 PIN_524110_19613 1549-8716-6404 08/07/02 13:40:06 casp5@bialko.llnl.gov PLEASE NOTE: Submission of a duplicate prediction (same target, format, model index) will REPLACE an existing submission (ACCESSION CODE), provided it is received before the target has expired. The current status of models accepted for target T0170 MODEL_INDEX PIN CODE DATE E-mail T0170SS389_1 PIN_524110_19613 1549-8716-6404 08/07/02 13:40:06 casp5@bialko.llnl.gov For more information on accepted models submitted to CASP5 see: http://PredictionCenter.llnl.gov/casp5/models/casp5-models.html Please check below if the verified data of your submission is correct. # Reading prediction format SS PFRMAT SS TARGET T0170 AUTHOR 1549-8716-6404 # Reading MODEL 1 # Reading prediction format SS (DONE) # Checking the SS prediction MODEL 1 # Checking the SS prediction MODEL 1 (DONE) # MODEL index: 1 # Total number of residues in model: 69 # Number of residues with nonzero confidence: 69 # Number of METHOD records: 65 # No errors. ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT SS TARGET T0170 AUTHOR 1549-8716-6404 METHOD CAFASP METHOD samt02_dssp_ehl METHOD This file is the result of combining several RDB files, specifically METHOD T0170.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0170.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0170.t2k.str.rdb (weight 1.53983) METHOD These files were combined by translating their predictions into EHL METHOD predictions with tables generated by compare-real, and then combining METHOD those predictions with weights proportional to their mutual information METHOD with the EHL alphabet. The comments from the individual files follow. METHOD METHOD Comments from T0170.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0170 METHOD Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 7 (1 EBGHSTL ) METHOD The input amino acid frequencies were determined from METHOD alignment T0170.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 30 METHOD METHOD ============================================ METHOD Comments from T0170.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0170 METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 6 (1 EBGHTL ) METHOD The input amino acid frequencies were determined from METHOD alignment T0170.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 30 METHOD METHOD ============================================ METHOD Comments from T0170.t2k.str.rdb METHOD ============================================ METHOD TARGET T0170 METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 13 (1 str ) METHOD The input amino acid frequencies were determined from METHOD alignment T0170.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 30 METHOD METHOD ============================================ MODEL 1 Q C 0.93 P C 0.64 A H 0.56 K H 0.69 K H 0.72 T H 0.71 Y H 0.69 T H 0.70 W H 0.62 N H 0.53 T H 0.59 K H 0.91 E H 0.94 E H 0.96 A H 0.95 K H 0.97 Q H 0.97 A H 0.96 F H 0.97 K H 0.97 E H 0.97 L H 0.96 L H 0.95 K H 0.89 E H 0.74 K C 0.58 R C 0.92 V C 0.90 P C 0.95 S C 0.93 N C 0.94 A C 0.88 S C 0.79 W H 0.89 E H 0.91 Q H 0.93 A H 0.92 M H 0.93 K H 0.93 M H 0.93 I H 0.90 I H 0.74 N C 0.49 D C 0.88 P C 0.65 R C 0.56 Y H 0.54 S H 0.52 A H 0.46 L C 0.53 A C 0.75 N C 0.86 L H 0.72 S H 0.85 E H 0.91 K H 0.94 K H 0.95 Q H 0.95 A H 0.95 F H 0.96 N H 0.97 A H 0.96 Y H 0.96 K H 0.94 V H 0.90 Q H 0.82 T H 0.64 E C 0.65 K C 0.97 END END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Tue Aug 13 12:46:28 2002 Date: Tue, 13 Aug 2002 12:46:22 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0170 TS samt02.pdb 1 X-SpamBouncer: 1.4 (10/07/01) X-SBNote: From Admin X-SBNote: FROM_DAEMON/Listserv X-SBPass: No Freemail Filtering X-SBClass: Admin # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Tue Aug 13 12:18:35 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_308962_22410 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0170TS189_1 Current information on models submitted in prediction T0170TS189 MODEL_INDEX PIN CODE DATE E-mail T0170TS189_1 PIN_308962_22410 5035-2079-5263 08/13/02 12:18:35 casp5@bialko.llnl.gov PLEASE NOTE: Submission of a duplicate prediction (same target, format, model index) will REPLACE an existing submission (ACCESSION CODE), provided it is received before the target has expired. The current status of models accepted for target T0170 MODEL_INDEX PIN CODE DATE E-mail T0170TS189_1 PIN_308962_22410 5035-2079-5263 08/13/02 12:18:35 casp5@bialko.llnl.gov For more information on accepted models submitted to CASP5 see: http://PredictionCenter.llnl.gov/casp5/models/casp5-models.html Please check below if the verified data of your submission is correct. # Reading prediction format TS PFRMAT TS TARGET T0170 AUTHOR 5035-2079-5263 # Reading MODEL 1 PARENT 1B2V_A # Loading PARENT structure: 1b2v (chain: A) # Number of residues in PARENT structure: 173 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 1 # IMPORTANT NOTE! Not complete main chain atoms for residue T 6 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # It is requested that coordinate data be supplied for at least # # all non-hydrogen main chain atoms, i.e. the N, CA, C and O # # atoms of every residue. Specifically, if only CA atoms are # # predicted by the method, predictors are encouraged to build # # the main chain atoms for every residue before submission to # # CASP. If only CA atoms were submitted it would not be possible # # to run most of the analysis software, which would severely # # limit the evaluation of that prediction. # # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # IMPORTANT NOTE! Not complete main chain atoms for residue Y 7 # IMPORTANT NOTE! Not complete main chain atoms for residue T 8 # IMPORTANT NOTE! Not complete main chain atoms for residue W 9 # IMPORTANT NOTE! Not complete main chain atoms for residue N 10 # IMPORTANT NOTE! Not complete main chain atoms for residue T 11 # IMPORTANT NOTE! Not complete main chain atoms for residue K 12 # IMPORTANT NOTE! Not complete main chain atoms for residue E 13 # IMPORTANT NOTE! Not complete main chain atoms for residue E 14 # IMPORTANT NOTE! Not complete main chain atoms for residue A 15 # IMPORTANT NOTE! Not complete main chain atoms for residue K 16 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 17 # IMPORTANT NOTE! Not complete main chain atoms for residue A 18 # IMPORTANT NOTE! Not complete main chain atoms for residue F 19 # IMPORTANT NOTE! Not complete main chain atoms for residue K 20 # IMPORTANT NOTE! Not complete main chain atoms for residue E 21 # IMPORTANT NOTE! Not complete main chain atoms for residue L 22 # IMPORTANT NOTE! Not complete main chain atoms for residue L 23 # IMPORTANT NOTE! Not complete main chain atoms for residue K 24 # IMPORTANT NOTE! Not complete main chain atoms for residue E 25 # IMPORTANT NOTE! Not complete main chain atoms for residue K 26 # IMPORTANT NOTE! Not complete main chain atoms for residue R 27 # IMPORTANT NOTE! Not complete main chain atoms for residue V 28 # IMPORTANT NOTE! Not complete main chain atoms for residue P 29 # IMPORTANT NOTE! Not complete main chain atoms for residue S 30 # IMPORTANT NOTE! Not complete main chain atoms for residue N 31 # IMPORTANT NOTE! Not complete main chain atoms for residue A 32 # IMPORTANT NOTE! Not complete main chain atoms for residue S 33 # IMPORTANT NOTE! Not complete main chain atoms for residue W 34 # IMPORTANT NOTE! Not complete main chain atoms for residue E 35 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 36 # IMPORTANT NOTE! Not complete main chain atoms for residue A 37 # IMPORTANT NOTE! Not complete main chain atoms for residue M 38 # IMPORTANT NOTE! Not complete main chain atoms for residue K 39 # IMPORTANT NOTE! Not complete main chain atoms for residue M 40 # IMPORTANT NOTE! Not complete main chain atoms for residue I 41 # IMPORTANT NOTE! Not complete main chain atoms for residue I 42 # Checking the TS prediction MODEL 1 (DONE) # MODEL index: 1 # Target name: T0170 # Total number of residues in target: 69 # Total number of residues in model: 37 # Total number of atoms in model: 37 # Number of atoms with 1.0 occupancy: 37 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 37 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0170 AUTHOR 5035-2079-5263 METHOD CAFASP MODEL 1 PARENT 1B2V_A ATOM 138 CA THR 6 7.529 -0.395 13.700 1.00 1.00 ATOM 139 CA TYR 7 10.256 -0.034 16.329 1.00 1.00 ATOM 140 CA THR 8 9.084 3.490 17.234 1.00 1.00 ATOM 141 CA TRP 9 5.628 1.913 17.693 1.00 1.00 ATOM 142 CA ASN 10 6.872 -0.999 19.843 1.00 1.00 ATOM 143 CA THR 11 6.153 -3.469 17.018 1.00 1.00 ATOM 144 CA LYS 12 9.147 -5.653 16.033 1.00 1.00 ATOM 145 CA GLU 13 7.165 -7.632 13.437 1.00 1.00 ATOM 146 CA GLU 14 8.774 -5.934 10.439 1.00 1.00 ATOM 147 CA ALA 15 12.326 -6.258 11.824 1.00 1.00 ATOM 148 CA LYS 16 11.819 -10.010 12.542 1.00 1.00 ATOM 149 CA GLN 17 10.585 -10.531 9.033 1.00 1.00 ATOM 150 CA ALA 18 13.645 -8.762 7.684 1.00 1.00 ATOM 151 CA PHE 19 15.943 -10.779 10.008 1.00 1.00 ATOM 152 CA LYS 20 14.344 -14.141 8.975 1.00 1.00 ATOM 153 CA GLU 21 15.166 -13.171 5.395 1.00 1.00 ATOM 154 CA LEU 22 18.823 -12.597 6.353 1.00 1.00 ATOM 155 CA LEU 23 19.041 -15.618 8.617 1.00 1.00 ATOM 156 CA LYS 24 17.462 -18.176 6.328 1.00 1.00 ATOM 157 CA GLU 25 20.810 -18.369 4.472 1.00 1.00 ATOM 158 CA LYS 26 22.453 -19.724 7.608 1.00 1.00 ATOM 159 CA ARG 27 19.574 -22.104 8.195 1.00 1.00 ATOM 160 CA VAL 28 18.483 -20.002 11.188 1.00 1.00 ATOM 161 CA PRO 29 15.601 -17.689 12.091 1.00 1.00 ATOM 162 CA SER 30 14.517 -15.269 14.836 1.00 1.00 ATOM 163 CA ASN 31 13.571 -18.327 16.894 1.00 1.00 ATOM 164 CA ALA 32 17.320 -19.150 17.031 1.00 1.00 ATOM 165 CA SER 33 19.282 -18.051 20.122 1.00 1.00 ATOM 166 CA TRP 34 22.059 -15.455 20.012 1.00 1.00 ATOM 167 CA GLU 35 24.598 -18.223 20.675 1.00 1.00 ATOM 168 CA GLN 36 23.297 -20.221 17.685 1.00 1.00 ATOM 169 CA ALA 37 23.569 -17.162 15.415 1.00 1.00 ATOM 170 CA MET 38 27.136 -16.378 16.635 1.00 1.00 ATOM 171 CA LYS 39 28.193 -19.986 15.894 1.00 1.00 ATOM 172 CA MET 40 26.841 -19.713 12.337 1.00 1.00 ATOM 173 CA ILE 41 28.064 -16.183 11.571 1.00 1.00 ATOM 174 CA ILE 42 31.501 -16.057 13.192 1.00 1.00 TER END ################################ # # # END # # # ################################ From mailer@bialko.llnl.gov Tue Aug 13 12:52:39 2002 Date: Tue, 13 Aug 2002 12:52:33 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu Subject: T0170 TS samt02.pdb 2 X-SpamBouncer: 1.4 (10/07/01) X-SBNote: From Admin X-SBNote: FROM_DAEMON/Listserv X-SBPass: No Freemail Filtering X-SBClass: Admin # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Tue Aug 13 12:24:45 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_368906_22428 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0170TS189_2 Current information on models submitted in prediction T0170TS189 MODEL_INDEX PIN CODE DATE E-mail T0170TS189_2 PIN_368906_22428 5035-2079-5263 08/13/02 12:24:45 casp5@bialko.llnl.gov T0170TS189_1 PIN_308962_22410 5035-2079-5263 08/13/02 12:18:35 casp5@bialko.llnl.gov PLEASE NOTE: Submission of a duplicate prediction (same target, format, model index) will REPLACE an existing submission (ACCESSION CODE), provided it is received before the target has expired. The current status of models accepted for target T0170 MODEL_INDEX PIN CODE DATE E-mail T0170TS189_1 PIN_308962_22410 5035-2079-5263 08/13/02 12:18:35 casp5@bialko.llnl.gov T0170TS189_2 PIN_368906_22428 5035-2079-5263 08/13/02 12:24:45 casp5@bialko.llnl.gov For more information on accepted models submitted to CASP5 see: http://PredictionCenter.llnl.gov/casp5/models/casp5-models.html Please check below if the verified data of your submission is correct. # Reading prediction format TS PFRMAT TS TARGET T0170 AUTHOR 5035-2079-5263 # Reading MODEL 2 PARENT 2IGD # Loading PARENT structure: 2igd (chain: ) # Number of residues in PARENT structure: 61 # Reading prediction format TS (DONE) # Checking the TS prediction MODEL 2 # IMPORTANT NOTE! Not complete main chain atoms for residue N 10 # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # It is requested that coordinate data be supplied for at least # # all non-hydrogen main chain atoms, i.e. the N, CA, C and O # # atoms of every residue. Specifically, if only CA atoms are # # predicted by the method, predictors are encouraged to build # # the main chain atoms for every residue before submission to # # CASP. If only CA atoms were submitted it would not be possible # # to run most of the analysis software, which would severely # # limit the evaluation of that prediction. # # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! # # IMPORTANT NOTE! Not complete main chain atoms for residue T 11 # IMPORTANT NOTE! Not complete main chain atoms for residue K 12 # IMPORTANT NOTE! Not complete main chain atoms for residue E 13 # IMPORTANT NOTE! Not complete main chain atoms for residue E 14 # IMPORTANT NOTE! Not complete main chain atoms for residue A 15 # IMPORTANT NOTE! Not complete main chain atoms for residue K 16 # IMPORTANT NOTE! Not complete main chain atoms for residue Q 17 # IMPORTANT NOTE! Not complete main chain atoms for residue A 18 # IMPORTANT NOTE! Not complete main chain atoms for residue F 19 # IMPORTANT NOTE! Not complete main chain atoms for residue K 20 # IMPORTANT NOTE! Not complete main chain atoms for residue E 21 # IMPORTANT NOTE! Not complete main chain atoms for residue L 22 # IMPORTANT NOTE! Not complete main chain atoms for residue L 23 # IMPORTANT NOTE! Not complete main chain atoms for residue K 24 # IMPORTANT NOTE! Not complete main chain atoms for residue E 25 # IMPORTANT NOTE! Not complete main chain atoms for residue K 26 # IMPORTANT NOTE! Not complete main chain atoms for residue R 27 # IMPORTANT NOTE! Not complete main chain atoms for residue V 28 # IMPORTANT NOTE! Not complete main chain atoms for residue P 29 # IMPORTANT NOTE! Not complete main chain atoms for residue S 30 # Checking the TS prediction MODEL 2 (DONE) # MODEL index: 2 # Target name: T0170 # Total number of residues in target: 69 # Total number of residues in model: 21 # Total number of atoms in model: 21 # Number of atoms with 1.0 occupancy: 21 # Number of fragments in model: 1 # Number of METHOD records: 1 # No errors. # Number of Warnings: 21 ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT TS TARGET T0170 AUTHOR 5035-2079-5263 METHOD CAFASP MODEL 2 PARENT 2IGD ATOM 26 CA ASN 10 7.260 14.854 9.299 1.00 1.00 ATOM 27 CA THR 11 10.612 16.526 10.001 1.00 1.00 ATOM 28 CA LYS 12 12.142 19.541 11.794 1.00 1.00 ATOM 29 CA GLU 13 12.712 21.542 8.632 1.00 1.00 ATOM 30 CA GLU 14 9.005 21.472 7.817 1.00 1.00 ATOM 31 CA ALA 15 8.121 22.548 11.353 1.00 1.00 ATOM 32 CA LYS 16 10.719 25.317 11.217 1.00 1.00 ATOM 33 CA GLN 17 9.139 26.736 8.061 1.00 1.00 ATOM 34 CA ALA 18 5.654 26.682 9.658 1.00 1.00 ATOM 35 CA PHE 19 6.940 28.471 12.774 1.00 1.00 ATOM 36 CA LYS 20 8.915 31.065 10.827 1.00 1.00 ATOM 37 CA GLU 21 5.784 31.817 8.802 1.00 1.00 ATOM 38 CA LEU 22 3.757 32.125 12.022 1.00 1.00 ATOM 39 CA LEU 23 6.322 34.523 13.495 1.00 1.00 ATOM 40 CA LYS 24 6.375 36.639 10.306 1.00 1.00 ATOM 41 CA GLU 25 2.536 36.702 10.145 1.00 1.00 ATOM 42 CA LYS 26 2.519 38.093 13.718 1.00 1.00 ATOM 43 CA ARG 27 5.296 40.638 13.264 1.00 1.00 ATOM 44 CA VAL 28 7.921 38.823 15.338 1.00 1.00 ATOM 45 CA PRO 29 11.526 39.426 14.290 1.00 1.00 ATOM 46 CA SER 30 13.865 37.643 16.623 1.00 1.00 TER END ################################ # # # END # # # ################################