Old schedules for Karplus bioinformatics lab
UC Santa Cruz

Spring 2011 individual meeting schedule

Only on campus MWThF (not T) this Spring.

time Monday Wednesday Thursday Friday
9:00 ----- ----- ----- -----
9:30
10:00
10:30 ----- ----- -----
11:00 BME 220 PSB305 BME 220 BME 220
11:30 BME 220 BME 220 BME 220
12:00 BME 220 BME 220 BME280B PSB305 BME 220
12:30 BME281K PSB305 BME280B
1:00 BME281K BME280B
1:30 ----- BME281K BME280B -----
2:00 BME235 PSB305 BME 235 Lauren Lui BME 235
2:30 BME235 BME 235 BME 235
3:00 BME235 BME 235 Andrew Holmes 235/faculty mtg PSB305
3:30 BME220L BE 287 Rasmus Fonseca faculty mtg
4:00 BME220L John Archie faculty mtg
4:30 BME220L bread-and-tea PSB 313
5:00 BME220L bread-and-tea
5:30 BME220L ----- ----- ----
6:00 BME220L ----- ----- ----
6:30 BME220L ----- ----- ----

Spring 2011 Group Meetings

Lab meetings will be in PSB 305 on Wednesdays 12–1:40. We're meeting jointly with Dietlind Gerloff's lab again this quarter.

datespeakertopic/paper
30 Mar 2011 3:30–4 Scheduling the quarter.
6 Apr 2011 ---Dietlind away, no meeting
13 Apr 2011 Dietlind Gerloff recap of previous week's meeting
20 Apr 2011 Jonathan Magasin Latent Semantic Indexing
Gary W. Stuart, Karen Moffett and Steve Bakerbr
Integrated gene and species phylogenies from unaligned whole genome protein sequences.
Bioinformatics 2002 18(1): 100-108.
doi:10.1093/bioinformatics/18.1.100
27 Apr 2011 Felicia Kemp
4 May 2011 --- Kevin away, no meeting
11 May 2011 John Archie molecular dynamics tutorial
18 May 2011 METX seminar CheZHP: a rogue phosphatase
Pam Lertsethtakarn
Graduate Student, Microbiology and Environmental Toxicology
25 May 2011 George Shackelford Random forests for secondary-structure prediction
1 June 2011 Rasmus? Jon? Eli?
8 June 2011 exam week no meeting

Winter 2011 individual meeting schedule

Only on campus MWThF (not T) this Winter.

time Monday Wednesday Thursday Friday
9:00 ----- ----- ----- -----
9:30
10:00 123B Dean BME281K PSB305
10:30 BME281K
11:00 Office "hour" BME281K office "hour"
11:30
12:00 BME280B PSB240
12:30 BME280B
1:00 123B Lopez BME280B
1:30 BME280B
2:00 123B Perrott 123B RED PSB 305
2:30 123B Hampton 1243B Lam 123B RED
3:00 John Archie Rasmus Fonseca faculty mtg PSB305
3:30 faculty mtg
4:00 123B circuits faculty mtg
4:30 --- 123B circuits bread-and-tea PSB 313
5:00 BME123B PSB305 bread-and-tea
5:30 ----- BME123B ----
6:00 ----- BME123B ----
6:30 ----- BME123B ----

Winter 2011 Group Meetings

Lab meetings will be in PSB 305 (the conference room) on Thursdays at 10:00 a.m. We're meeting jointly with Dietlind Gerloff's lab again this quarter.

datespeakertopic/paper
6 Jan 2011 --- Scheduling the quarter. Discussed possible revisions to the design of the BME 220 Protein Informatics class in the spring.
13 Jan 2011 --- Cancelled. Dietlind out of town.
20 Jan 2011 George Shackelford Movshovitz-Attias D, London N, Schueler-Furman O.
On the use of structural templates for high-resolution docking.
Proteins. 2010 Jun;78(8):1939-49. doi:10.1002/prot.22710
27 Jan 2011 Felicia Kemp Maik Veelders, Stefan Brückner, Dimitri Ott, Carlo Unverzagt, Hans-Ulrich Mösch, Lars-Oliver Essen
Structural basis of flocculin-mediated social behavior in yeast
PNAS 107(52):22511-22516, December 28, 2010.
doi: 10.1073/pnas.1013210108
3 Feb 2011 Judging Westlake Science Fair
10 Feb 2011 Rasmus Fonseca research in progress
17 Feb 2011 John Archie molecular dynamics techniques
24 Feb 2011 Jonathan Magasin practice for advancement
3 Mar 2011 John Archie practice for advancement
10 Mar 2011 No meeting (scheduling mixup)
17 Mar 2011 exam week

Fall 2010 individual meeting schedule

Only on campus MWThF (not T) this Fall.

time Monday Wednesday Thursday Friday
9:00 ----- ----- ----- -----
9:30
10:00
10:30 office hours John Archie
11:00 office hours
11:30
12:00 --- --- BME280B PSB305 ---
12:30 BME123A JBE156 BME123A JBE156 BME280B BME123A JBE156
1:00 BME123A BME123A BME280B BME123A
1:30 BME123A BME123A BME280B BME123A
2:00 BME205 PSB305 BME205 PSB305 (BME207?) PSB305BME205 PSB305
2:30 BME205 BME205 (BME207?) BME205
3:00 BME205 BME205 (BME207?) BME205/faculty
3:30 BME281G/K PSB305 (BME207?) faculty mtg PSB305
4:00 BME281G/K Rasmus FonsecaBME200 PSB305 faculty mtg
4:30 BME281G/K BME200 bread-and-tea PSB 313
5:00 BME200 bread-and-tea
5:30 ----- ---- BME200 ----

Fall 2010 Group Meetings

Lab meetings will be in PSB 305 (the conference room) on Mondays at 3:30 . We're meeting jointly with Dietlind Gerloff's lab again this quarter.

datespeakertopic/paper
Fri 24 Sept 2010 9:30Kevin Karplus Vladimir Potapov, Mati Cohen, Yuval Inbar, and Gideon Schreiber
Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions
BMC Bioinformatics 2010, 11:374 doi:10.1186/1471-2105-11-374
4 Oct 2010 Dietlind Gerloff James Wasmuth, Jennifer Daub, José Manuel Peregrín-Alvarez, Constance A.M. Finney, and John Parkinson
The origins of apicomplexan sequence innovation
Genome Research 2009. 19: 1202-1213
doi: 10.1101/gr.083386.108
11 Oct 2010 No meeting.
Wed 13 Oct 2010 6pmThomas Juetteman practice
Thurs 14 Oct 2010 2pmThomas Juetteman (in Camilla's class)
18 Oct 2010 Rasmus Fonseca Ranking beta sheets
25 Oct 2010 Dietlind Gerloff An Vo, Nha Nguyen, and Heng Huang
Solenoid and non-solenoid protein recognition using stationary wavelet packet transform.
Bioinformatics 26(18): i467–i473, 2010. doi:10.1093/bioinformatics/btq371
1 Nov 2010 John Archie Dahiyat BI and Mayo SL.
De novo protein design: fully automated sequence selection.
Science. 1997 Oct 3;278(5335):82-7.
doi:10.1126/science.278.5335.82
8 Nov 2010 Jonathan Magasin a low-bandwidth strategy to help determine taxonomy/function of unassigned (e.g., no significant nr hits) marine metatranscriptomic reads by comparing them to metagenomic contigs. Reads and contigs are stored in local labs' databases, with labs acting as peers in an OpenKnowledge network.
15 Nov 2010 Chris Wilks Aiding Plasmodium falciparum gene finding with MAINE/FAIRE experimental signal data through the use of random forests.
22 Nov 2010 no meeting (Gerloff unavailable)
30 Nov 2010 Felicia Kemp and Edward Liaw presentations on current research projects

Summer 2010 individual meeting schedule

Only on campus TTh over the summer. Currently no weekly meetings, but I'll be generally available on Tuesdays and Thursdays (except July 6–16, when I'll be in Boston for ISMB).

Summer 2010 Group Meetings

There will be no group meetings this summer. Group meetings will resume in the Fall (perhaps jointly with Dietlind's group again).

Spring 2010 individual meeting schedule

Only on campus MWThF (not T) this Spring.

time Monday Wednesday Thursday Friday
9:00 ----- ----- ----- -----
9:30
10:00 John Archie office hours metagenomics E&MS C332
10:30 John Archie office hours metagenomics E&MS C332
11:00
11:30 Jeff Long
12:00 BME280B
12:30 BME280B
1:00 BME280B
1:30 --- --- BME280B ---
2:00 BME 235 BME 235 Grant Thiltgen BME 235
2:30 BME 235 BME 235 Grant ThiltgenBME 235
3:00 BME 235 BME 235 faculty PSB305
3:30 BME 281G/K faculty mtg
4:00 BME 281G/K faculty mtg
4:30 George Shackelfordbread-and-tea PSB 313 faculty mtg
5:00 bread-and-tea
5:30 ----- ---- bread-and-tea ----

Spring 2010 Group Meetings

Lab meetings will be in PSB 305 (the conference room) on Wednesdays at 3:30 (after BME 235). We're meeting jointly with Dietlind Gerloff's lab again this quarter.

datespeakertopic/paper
31 Mar 2010 George Shackelford Leo Breiman
Random Forests
Machine Learning 45(1):5-32, October, 2001.
doi: 10.1023/A:1010933404324
7 Apr 2010 Grant Thiltgen Andrew D. Fernandes and Gregory B. Gloor
Mutual Information is Critically Dependent on Prior Assumptions: Would the Correct Estimate of Mutual Information Please Identify Itself?
Bioinformatics, doi:10.1093/bioinformatics/btq111
14 Apr 2010 Kevin Karplus Will Sheffler and David Baker
RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation
Protein Science 18:229-239 (2009). http://www.proteinscience.org/details/journalArticle/110975/RosettaHoles_Rapid_assessment_of_protein_core_packing_for_structure_prediction_r.html
doi: 10.1002/pro.8
21 Apr 2010 Grant absent (no meeting)
28 Apr 2010 John Archie Maria L. Garcia.
Ion Channels: Gate Expectations.
Nature. 2004 July 8; 430(6996):153-155.
doi:10.1038/430153a

Stefan Becker and Heinrich Terlau.
Toxins from Cone Snails: Properties, Applications and Biotechnological Production.
Applied Microbiology and Biotechnology. 2008 May; 79(1):1-9 (2008).
doi:10.1007/s00253-008-1385-6
5 May 2010 Grant Thiltgen Jonathan J Ellis, Fabien PE Huard, Charlotte M Deane, Sheenal Srivastava, Graham R Wood.
Directionality in protein fold prediction
BMC Bioinformatics 2010, 11:172
doi:10.1186/1471-2105-11-172
12 May 2010 Kevin Karplus
19 May 2010 Kevin absent (no meeting)
26 May 2010 Thomas Juettemann practice talk: BISC: Binary SubComplexes in Proteins Database
2 Jun 2010 George Shackleford Short talk on some results using CS-Blast for single-stage contact prediction.
also 2 Jun 2010 John Archie Jonathan W. Neidigh, R. Matthew Fesinmeyer, and Niels H. Andersen.
Designing a 20-Residue Protein.
Nature Structural Biology. 2002 June; 9(6):425--430.
doi:10.1038/nsb798
9 Jun 2010 exam week (no meeting)

Winter 2010 individual meeting schedule

Only on campus MWThF (not T) this Winter.
time Monday Wednesday Thursday Friday
9:00 ----- ----- ----- -----
9:30
10:00
10:30
11:00
11:30 Bert Linderkamp
12:00 BME280B
12:30 Adam Rogers BME280B
1:00 iRAGE BME280B
1:30 iRAGE BME280B Samantha Downey
2:00 Jeff Long Grant T. BME 281G/K .
2:30 Grant T. BME 281G/K
3:00 Chuck Chan BME 281G/K faculty PSB305
3:30 Chris BrumbaughMax Cherf George S. faculty mtg
4:00 John A. Melissa Eberle faculty mtg
4:30 John A. ----- bread-and-tea PSB 313 faculty mtg
5:00 BME 123B JBE165bread-and-tea
5:30 ----- BME 123B bread-and-tea
6:00 ----- BME 123B -----
6:30 ----- BME 123B -----

Winter 2010 Group Meetings

Lab meetings will be in PSB 305 (the conference room) on Thursdays at 2 p.m. (after BME 280B). We're meeting jointly with Dietlind Gerloff's lab this quarter.

date speaker topic/paper
7 Jan 2010 Grant Thiltgen Rahat O, Alon U, Levy Y, Schreiber G
Understanding hydrogen-bond patterns in proteins using network motifs.
Bioinformatics 2009 Nov 15 25:2921-8
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp541 doi:10.1093/bioinformatics/btp541
14 Jan 2010 scheduling, discussion of conferences, Kevin Karplus presented recent results in assembly and mapping for next-generation sequencing
21 Jan 2010 Jonathan Magasin Biao Li, Vidhya G. Krishnan, Matthew E. Mort, Fuxiao Xin, Kishore K. Kamati, David N. Cooper, Sean D. Mooney, and Predrag Radivojac
Automated inference of molecular mechanisms of disease from amino acid substitutions.
Bioinformatics 2009 Nov 1 25:2744&ndsh;2750.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp528
doi:10.1093/bioinformatics/btp528
28 Jan 2010 Herbert Lee Nasidze I, Li J, Quinque D, Kun T, and Stoneking M.
Global Diversity in the Human Salivary Microbiome
Genome Research 2009, 19: 636-643.
http://genome.cshlp.org/content/19/4/636 doi: 10.1101/gr.084616.108
4 Feb 2010 no presentation, discussed possible grant projects
11 Feb 2010 no presentation, discussed external review
18 Feb 2010 external review
25 Feb 2010 Chris Brumbaugh Mark P Styczynski, Kyle L Jensen, Isidore Rigoutsos, Gregory Stephanopoulos
BLOSUM62 miscalculations improve search performance
Nature Biotechnology 26, 274-275 (2008)
doi: 10.1038/nbt0308-274
http://www.nature.com/nbt/journal/v26/n3/full/nbt0308-274.html
4 Mar 2010 Thomas Juettemann Qifang Xu, Adrian A. Canutescu, Guoli Wang, Maxim Shapovalov, Zoran Obradovic, and Roland L. Dunbrack Jr.
Statistical Analysis of Interface Similarity in Crystals of Homologous Proteins
Journal of Molecular Biology 381(2):487-507, 29 August 2008
doi:10.1016/j.jmb.2008.06.002
11 Mar 2010 John Archie Yaminsky, Vassili V. and Vogler, Erwin A.
Hydrophobic Hydration.
Curr Opin Colloid Interface Sci 6(4): 342--349.
doi:10.1016/S1359-0294(01)00104-2
18 Mar 2010 exam week (no meeting)

Fall 2009 individual meeting schedule

Only on campus MWThF (not T) this fall.

time Monday Wednesday Thursday Friday
9:00 ----- ----- ----- -----
9:30
10:00
10:30 Grant T. Open Office
11:00 Grant T. Open Office BME281G/K
11:30 BME281G/K
12:00 ----- ----- BME280B BME281G/K
12:30 BME123A BME123A BME280B BME123A
1:00 BME123A BME123A BME280B BME123A
1:30 BME123A BME123A BME280B BME123A
2:00 BME205 BME205 George S. BME205
2:30 BME205 BME205 BME205
3:00 BME205 BME205 BME205
3:30 faculty PSB305
4:00 John Archie BME200 bread-and-tea PSB 313
4:30 BME200 bread-and-tea
5:00 BME200 bread-and-tea
5:30 BME200

Fall 2009 Group Meetings

Lab meetings will be in PSB 305 (the conference room) on Fridays at 11 a.m. We're meeting jointly with Dietlind Gerloff's lab this quarter.

datespeakertopic/paper
25 Sep 2009 organizational meeting
2 Oct 2009 Grant Thiltgen Tyagi M, Bornot A, Offmann B, de Brevern AG.
Protein short loop prediction in terms of a structural alphabet.
Comput Biol Chem. 2009 Aug;33(4):329-33. Epub 2009 Jun 25.
PMID: 19625218 doi:10.1016/j.compbiolchem.2009.06.002

A.G. de Brevern, C. Etchebest, S. Hazout
Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks
Proteins: Structure, Function, and Bioinformatics Volume 41 Issue 3, Pages 271 - 287
doi: 10.1002/1097-0134(20001115)41:3<271::AID-PROT10>3.0.CO;2-Z

9 Oct 2009 Lynn Olson rotation plan
16 Oct 2009 Herbert Lee summer project
23 Oct 2009 face-to-face meetings with grad committee
30 Oct 2009 Elevator practice talks
6 Nov 2009 Jonathan Magasin intro to proteomics
13 Nov 2009 Jonathan Magasin intro to proteomics continued
20 Nov 2009 George Shackelford ISMB 3d-SIG 2008 talk
27 Nov 2009 Thanksgiving break no meeting
4 Dec 2009 John Archie Günterrt P. Automated NMR structure calculation with CYANA. Methods Mol Biol. 2004;278:353-78.
doi:10.1385/1-59259-809-9:353
11 Dec 2009 (exam week)

Summer 2009 individual meeting schedule

Only on campus TTh over summer.

time Tuesday Thursday
9:00 ----- -----
9:30
10:00 John Archie
10:30 John Archie
11:00
11:30
12:00
12:30
1:00
1:30
2:00 Grant Thiltgen
2:30 Grant Thiltgen
3:00 Josue Samayoa
3:30 Josue SamayoaGeorge Shackelford
4:00 summer bread and tea
4:30 summer bread and tea
5:00 summer bread and tea
5:30 ---- ----

Summer 2009 Group Meetings

The lab meetings normally held in PSB 305 (the conference room) on Thursdays at 2:00 p.m. after BME 280B, but will not be held for summer 2009.

Spring 2009 individual meeting schedule

Only on campus MWThF (not Tues) this spring.

time Monday Wednesday Thursday Friday
9:00 ----- ----- ----- -----
9:30
10:00 John Archie
10:30 ----- ----- John Archie -----
11:00 BME 220 BME 220 BME 220
11:30 BME 220 BME 220 Rachel BinghamBME 220
12:00 BME 220 BME 220 BME280B PSB305BME 220
12:30 MCD seminar?structure club (1st Wed)BME280B MCD seminar?
1:00 MCD seminar?structure clubBME280B MCD seminar?
1:30 ---? ----- BME280B
2:00 Jeff FergusonGrant ThiltgenBME 281K PSB305 BME 281G
2:30 Grant ThiltgenBME 281K PSB305 BME 281G
3:00 Josue SamayoaBME 281K PSB305 faculty PSB305
3:30 Kwok Josue SamayoaGeorge Shackelford faculty PSB305
4:00 Chem seminar?Chem seminar?Michael Cusack bread-and-tea PSB 313
4:30 Chem seminar?Chem seminar? bread-and-tea
5:00 bread-and-tea
5:30 ---- ---- ---- ----

Spring 2009 Group Meetings

Lab meetings will be in PSB 305 (the conference room) on Thursdays at 2:00 p.m. will not be held over summer.
datespeakertopic/paper
26 March 2009 Break (no meeting)
WED. 1 Apr 2009 NO STRUCTURE CLUB
2 April 2009 Grant Thiltgen C Do, S Gross, S Batzoglou
CONTRAlign: Discriminative Training for Protein Sequence Alignment
Tenth Annual International Conference on Computational Molecular Biology (RECOMB)
2006 http://www.stanford.edu/~ssgross/contralign.pdf
9 April 2009 Josue Samayoa practice job talk
16 April 2009 Brian Raney defense 2pm E2-599
23 April 2009 John Archie useful tools (found or created)
30 April 2009 ??? what did we do?
WED. 6 May 2009 STRUCTURE CLUB 12:30 PSB 305
7 May 2009 no meeting:Kevin in Dublin
14 May 2009 Tony Capra, E2 599, 2-3:30 Using protein sequence, structure, and interactions to understand how proteins accomplish their functions.
FRI 15 May 2009 GRAD RESEARCH SYMPOSIUM
2-4 University Center (reception 4-5)
21 May 2009 no meeting (1/2 the lab out of town)
28 May 2009 updates on everyone's writing projects
WED. 3 June 2009 Matt Weirauch defense 12:30, PSB 305
4 June 2009 12th Annual UNDERGRADUATE RESEARCH SYMPOSIUM, Engineering Courtyard, 2-4
TUES 9 June 2009BME 220 poster session 4–7 pm PSB 305
11 June 2009 Grant Thiltgen recent work on new local-structure alphabets (also instructor evaluations)

Winter 2009 individual meeting schedule

Only on campus MWThF (not Tues) this winter.

time Monday Wednesday Thursday Friday
9:00 ----- ----- ----- -----
9:30
10:00 Javier John Archie
10:30 Javier John Archie
11:00
11:30
12:00 BME280B PSB240
12:30 MCD seminar?structure club (1st Wed)BME280B MCD seminar?
1:00 MCD seminar?structure clubBME280B MCD seminar?
1:30 ----- BME280B
2:00 Grant BME 281K PSB305 BME 281G
2:30 Grant BME 281K PSB305 BME 281G
3:00 Josue BME 281K PSB305 faculty PSB305
3:30 Josue George faculty PSB305
4:00 Chem seminar?Chem seminar?Alex bread-and-tea PSB 313
4:30 Chem seminar?Chem seminar? bread-and-tea
5:00 bread-and-tea
5:30 ---- ---- ---- ----

Winter 2009 Group Meetings

Lab meetings will be in PSB 305 (the conference room) on Thursdays at 2:00 p.m. after BME 280B.

Fall 2008 individual meeting schedule

Only on campus MTWF (not Th) this fall.

datespeakertopic/paper
WED. 7 Jan 2009 STRUCTURE CLUB 12:30 PSB 305
8 Jan 2009 Karplus, Shackleford, Archie CASP8 retrospective
15 Jan 2009 John Archie aims of knottin grant proposal
22 Jan 2009 Chirag Sharma Mallam AL, Onuoha SC, Grossmann JG, Jackson SE.
Knotted fusion proteins reveal unexpected possibilities in protein folding.
Mol Cell. 2008 Jun 5;30(5):642-8.
http://www.molecule.org/content/article/abstract?uid=PIIS109727650800244X
doi:10.1016/j.molcel.2008.03.019
29 Jan 2009 George Shackelford S.D. Dunn, L.M. Wahl, and G.B. Gloor
Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
Bioinformatics 2008 24(3):333-340;
doi:10.1093/bioinformatics/btm604

Rodrigo Gouveia-Oliveira and Anders Pedersen
Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation
Algorithms for Molecular Biology 2(1):12, 2007.
doi:10.1186/1748-7188-2-12

5 Feb 2009 Josue Samayoa finding new short proteins
12 Feb 2009 Grant Thiltgen A. Biegert and Johannes Söding
Sequence context-specific amino acid similarities for protein sequence comparison
Proc Natl Acad Sci USA 2009, doi:10.1073/pnas.0810767106 (preprint http://www.lmb.uni-muenchen.de/soeding/pdf/csblast_paper_pnas-R1.pdf )
19 Feb 2009 Kevin N-Cα-C bond angle, new undertaker ResidueFeature class, proposed new CostFunction class
26 Feb 2009 No meeting (305 used for ABI meeting)
WED. 4 Mar 2009 STRUCTURE CLUB 12:30 PSB 305 (Phil Berman)
5 March 2009 John Archie Jonathan W. Neidigh, R. Matthew Fesinmeyer, and Niels H. Andersen
Designing a 20-residue protein.
Nature Structural Biology 9, 425 - 430 (2002)
http://www.nature.com/nsmb/journal/v9/n6/full/nsb798.html
12 March 2009 Javier Castellanos results of internship
19 March 2009 George Shackelford (exam week) Vinson JP, DeCaprio D, Pearson MD, Luoma S, Galagan JE
Comparative Gene Prediction using Conditional Random Fields
Advances in Neural Information Processing Systems 19, 2007 B. Schölkopf and J. Platt and T. Hoffman, editors. MIT Press, Cambridge, MA. 1441--1448. http://books.nips.cc/papers/files/nips19/NIPS2006_0133.pdf

David DeCaprio, Jade P. Vinson, Matthew D. Pearson, et al.
Conrad: Gene prediction using conditional random fields
Genome Res. 2007 17: 1389-1398 originally published online August 9, 2007 doi:10.1101/gr.6558107

26 March 2009 Break (no meeting)
time Monday Tuesday Wednesday Friday
9:00 ----- ----- ----- -----
9:30
10:00 phone officeJohn A.
10:30 Open Office George
11:00 Grant Open Office BME 281G
11:30 Grant BME 281G
12:00 Josue BME280B PSB305 BME 281G
12:30 Josue BME280B structure club PSB305
1:00 BME280B structure club(1st Wed)
1:30 ----- BME280B ----- -----
2:00 BME205, E2#506BME 281K PSB305 BME205 BME205
2:30 BME205, E2#506BME 281K BME205 BME205
3:00 BME205, E2#506BME 281K BME205 BME205
3:30 (BME205 section)faculty PSB305
4:00 Alex BME200 PSB305BME205 section)bread-and-tea PSB 313
4:30 Chirag BME200 (BME205 section)bread-and-tea
5:00 BME200 bread-and-tea
5:30 BME200

Fall 2008 Group Meetings

Lab meetings will be in PSB 305 (the conference room) on Tuesdays, right after BME 280B.
datespeakertopic/paper
29 Sep 2008 organizational meeting
1 Oct 2008 STRUCTURE CLUB 12:30 PSB 305
7 Oct 2008 John Kim Dunbrack RL, Cohen FE
Bayesian statistical analysis of protein side-chain rotamer preferences.
Protein Science 1997 Aug 6 (8):1661-81
http://www.proteinscience.org.oca.ucsc.edu/cgi/content/abstract/6/8/1661
view F1000 comments http://www.f1000biology.com/article/id/1119124/evaluation
14 Oct 2008 Alex Atkins Vanita D. Sood and David Baker.
Recapitulation and Design of Protein Binding Peptide Structures and Sequences.
Journal of Molecular Biology Volume 357, Issue 3, 31 March 2006, Pages 917-927.
doi:10.1016/j.jmb.2006.01.045
21 Oct 2008 Chirag Sharma Yongpan Yana and John Moult
Protein Family Clustering for Structural Genomics
Journal of Molecular Biology, 28 October 2005, pp. 744-759
doi:10.1016/j.jmb.2005.08.058

Michael Levitt
Growth of novel protein structural data
PNAS February 27, 2007 vol. 104 no. 9 3183-3188
Published online before print February 20, 2007, doi:10.1073/pnas.0611678104

28 Oct 2008 Josue Samayoa
4 Nov 2008 Grant Thiltgen Shuai Cheng Li, Dongbo Bu, Xin Gao, Jinbo Xu, and Ming Li
Designing succinct structural alphabets
Bioinformatics 2008 24: i182-i189;
doi:10.1093/bioinformatics/btn165 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/13/i182?etoc
Tues 4 Nov 2008 Rachel Karchin, Etox seminar e-tox seminar site
5 Nov 2008 STRUCTURE CLUB 12:30 PSB 305
11 Nov 2008 NO UCSC (Veteran's Day)
18 Nov 2008 George Shackelford Philip Bradley, David Baker.
Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation.
Proteins: Structure, Function, and Bioinformatics 65(4):922-929, 2006.
doi:10.1002/prot.21133
25 Nov 2008
2Dec 2008 no meeting (CASP8)y
3 Dec 2008 STRUCTURE CLUB 12:30 PSB 305
9 Dec 2008 (exam week)

Summer 2008 individual meeting schedule

Only on campus MWF for summer, and I'll be very busy with CASP8 this summer (60- to 70-hour work weeks).

time Monday Wednesday Friday
10:00
10:30
11:00
11:30
12:00 John Archie?
12:30 CASP8 meeting
1:00 Josue? CASP8 meeting
1:30 Josue? CASP8 meeting
2:00 Firas? Grant?
2:30 Firas? Grant?
3:00
3:30 BME 281K BME 281G?
4:00 BME 281K BME 281G? bread and tea
4:30 BME 281K bread and tea
5:00 bread and tea
5:30

Summer 2008 Group Meetings

Lab meetings will be Mondays 3:00-4:30 in PSB 305 (the conference room).
datespeakertopic/paper
16 June 2008 Eric Anderson MCMC tutorial 1:30-4:30 Room 188 National Marine Fisheries Service Lab
Wed 18 June 2008 Kevin Karplus Organizing for summer (CASP8 intro)
23 June 2008
30 June 2008 John McGuffin LJ.
Benchmarking consensus model quality assessment for protein fold recognition.
BMC Bioinformatics. 2007 Sep 18;8:345.
doi:10.1186/1471-2105-8-345

McGuffin LJ, Jones DT.
Benchmarking secondary structure prediction for fold recognition.
Proteins. 2003 Aug 1;52(2):166-75.
doi:10.1002/prot.10408

7 July 2008 10am Kevin Karplus SURF-IT talk E2-215
7 July 2008 Kevin Karplus latest CASP results, particularly T0472
Fri 11 July 2008Firas KhatibThesis defence 12:30
14 July 2008 1pm Kevin Karplus talk for MBRS/MARC/CAMP students, Sinsheimer 123
14 July 2008 cancelled for strike
21 July 2008 Josue? recent results and new directions
28 July 2008 Firas report on Rosetta conference:
Bin Qian, Srivatsan Raman, Rhiju Das, Philip Bradley, Airlie J. McCoy, Randy J. Read, and David Baker
High-resolution structure prediction and the crystallographic phase problem
Nature 450, 259-264 (8 November 2007)
doi:10.1038/nature06249
http://www.nature.com/nature/journal/v450/n7167/abs/nature06249.html
4 August 2008 Chirag Christopher S. Miller and David Eisenberg
Using inferred residue contacts to distinguish between correct and incorrect protein models
Bioinformatics 2008 24: 1575-1582;
doi:10.1093/bioinformatics/btn248 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/14/1575?etoc
11 August 2008 NO MEETING (Kevin's Dad visiting)
18 August 2008 Allison results for summer
25 August 2008 George ????
1 September 2008 Labor Day no meeting
8 September 2008 Grant Rosemarie Swanson, Ioannis Kagiampakis, Jerry W. Tsai.
An Information Measure of the Quality of Protein Secondary Structure Prediction
Journal of Computational Biology 15(1): 65-79. January 1, 2008.
doi:10.1089/cmb.2007.0199
15 September 2008 Kevin Thomas P. Treynor, Christina L. Vizcarra, Daniel Nedelcu, and Stephen L. Mayo
Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function
PNAS | January 2, 2007 | vol. 104 | no. 1 | 48-53
http://www.pnas.org/cgi/content/full/104/1/48
22 September 2008 NO MEETING

Spring 2008 individual meeting schedule

(Note: not on campus on Thursdays this quarter.)

time Monday Tuesday Wednesday Friday
10:00 COT(Kerr129)
10:30 COT(Kerr129)
11:00 COT(Kerr129) John Kim
11:30 COT(Kerr129) Steven Hobbs
12:00 BME 280B John Archie
12:30 BME 280B
1:00 Josue BME 280B
1:30 Josue BME 280B
2:00 Firas George ?? Grant Open office
2:30 Firas George ?? Grant Open Office
3:00 BME 281K BMEfac
3:30 BME 281K BME 281G BMEfac
4:00 BME 281K BME 281G bread and tea
4:30 Alex Atkins bread and tea
5:00 bread and tea
5:30

Spring 2008 Group Meetings

Lab meetings will be Mondays 3:00-4:30 in PSB 305 (the conference room).
datespeakertopic/paper
31 March 2008 Glenn Millhauser Task classifying GPCRs
7 April 2008 Josue Samayoa Daniela Röthlisberger, Olga Khersonsky, Andrew M. Wollacott, Lin Jiang, Jason DeChancie, Jamie Betker, Jasmine L. Gallaher, Eric A. Althoff, Alexandre Zanghellini, Orly Dym, Shira Albeck, Kendall N. Houk, Dan S. Tawfik, David Baker
Kemp elimination catalysts by computational enzyme design.
Nature advance online publication 19 March 2008
doi:10.1038/nature06879
14 April 2008 John Archie Jian Qiu, Will Sheffler, David Baker, William Stafford Noble.
Ranking predicted protein structures with support vector regression.
Proteins: Structure, Function, and Bioinformatics 2007
DOI: 10.1002/prot.21809
21 April 2008 Martin Madera
Wed 23 Apr 2008 Janine Ilagan (Jurica lab) STRUCTURE CLUB Sinsheimer 123 12:30-1:40
28 April 2008 Firas Khatib practice interview
5 May 2008 Alex Atkins Johannes Söding
Protein homology detection by HMM-HMM comparison
Bioinformatics 2005 21(7):951-960;
doi:10.1093/bioinformatics/bti125
12 May 2008 John Kim Jesper Lundstr&ounl;m, Leszek Rychlewski, Janusz Bujnicki, and Arne Elofsson.
Pcons: A neural-networkbased consensus predictor that improves fold recognition
Protein Science (2001), 10:2354-2362. http://www.proteinscience.org/cgi/content/abstract/10/11/2354
Fri 16 May 2008 Grad research symposium
19 May 2008 California State Science Fair no meeting
26 May 2008 Memorial Day no meeting
Wed 28 May 2008 Eva and Danielle (Rubin lab) STRUCTURE CLUB Sinsheimer 123 12:30-1:40
Wed 28 May 2008 Bernick Advancement PSB 305 1-4
Fri30 May 2008 Thiltgen Advancement PSB 305 12-2
2 June 2008 Steven Hobbs back propagation
Thu 5 June 2008 Undergrad poster symposium

Winter 2008 individual meeting schedule

(Note: not on campus on Thursdays this Winter.)

time Monday Tuesday Wednesday Friday
10:00 COT(Kerr129) Stephanie
10:30 COT(Kerr129) Steven Hobbs
11:00 COT(Kerr129)
11:30 Firas COT(Kerr129)
12:00 Firas BME 280B
12:30 Grant BME 280B John A. Martin
1:00 Grant BME 280B John A. Martin
1:30 .. BME 280B .. ..
2:00 BME 220 George BME 220 BME 220
2:30 BME 220 George BME 220 BME 220
3:00 .. Josue .. BMEfac
3:30 BME 281K Josue BME 281G BMEfac
4:00 BME 281K Alex BME 281G bread and tea
4:30 .. Lauren bread and tea
5:00 Andy bread and tea
5:30

Winter 2008 Group Meetings

Lab meetings will be Mondays 3:30-4:40 in PSB 305 (the conference room).
datespeakertopic/paper
7 Jan 2008 administrivia
14 Jan 2008 Martin Madera Alignment test suite
14 Jan 2008 Josue Huaiqiu Zhu, Gang-Qing Hu, Yi-Fan Yang, Jin Wang, and Zhen-Su She
MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes
BMC Bioinformatics. 2007; 8: 97. http://www.biomedcentral.com/1471-2105/8/97
21 Jan 2008 No meeting
23 Jan 2008 Thomas Juettemann (Gerloff lab) STRUCTURE CLUB PSB 240 12:30-1:40
28 Jan 2008 Kevin new calibration method for HMMs
4 Feb 2008 Kevin brainstorming for grant renewal
11 Feb 2008 Richard Hughey SAM internals
18 Feb 2008 No meeting
25 Feb 2008 John Kim Narcis Fernandez-Fuentes, Brajesh K. Rai, Carlos J. Madrid-Aliste, J. Eduardo Fajardo, and Andras Fiser.
Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments.
Bioinformatics 23: 2558-2565, (2007)
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/19/2558
27 Feb 2008 Mira Patel (Millhauser lab) STRUCTURE CLUB PSB 341 12:30-1:40
3 Mar 2008 Steven Hobbs
  • Ke Chen and Lukasz Kurgan.
    PFRES: protein fold classification by using evolutionary information and predicted secondary structure.
    Bioinformatics 2007 23: 2843-2850.
    http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/21/2843
    • 10 Mar 2008 Grant practice for advancement
    17 Mar 2008 BME 220 class BME 220 poster session

    Fall 2007 individual meeting schedule

    (Note: not on campus on Thursdays this Fall.)

    time Monday Tuesday Wednesday Friday
    10:00 COT(Kerr129)
    10:30 COT(Kerr129)
    11:00 BME 205 COT(Kerr129) BME 205 BME 205
    11:30 BME 205 BME 205 BME 205
    12:00 BME 280B
    12:30 Open Office BME 280B George BME 281G
    1:00 Grant BME 280B George BME 281G
    1:30 Grant BME 280B
    2:00 Josue (BME 225) Martin M. Firas
    2:30 (BME 225) Martin M. Firas
    3:00 John (BME 225) group meetingBMEfac
    3:30 John (BME 225) group meetingBMEfac
    4:00 Martin P. BME 200 group meetingbread and tea
    4:30 Martin P. BME 200 Open office bread and tea
    5:00 BME 200 bread and tea
    5:30 BME 200

    Fall 2007 Group meetings

    Lab meetings will be Wednesdays 3-4:30 in     PSB 305 (the conference room).
    datespeakertopic/paper
    12 Sept 2007 Kevin Karplusrecent ideas: correlation between cost functions and real cost, new local structure alphabets, new calibration method for HMMs
    19 Sept 2007 Grant Thiltgen Ingo Ruczinski, Charles Kooperberg, Richard Bonneau, David Baker.
    Distributions of Beta Sheets in Proteins With Application to Structure Prediction
    Proteins: Structure Function and Genetics 48(1):85-87, 3 May 2002
    doi:10.1002/prot.10123
    http://depts.washington.edu/bakerpg/papers/Ruczinski-Proteins-v48-p85.pdf
    26 Sept 2007 Martin Paluszewski Shapovalov, M. V. and Dunbrack, R. L. Jr. Statistical and conformational analysis of the electron density of protein side-chains. Proteins 66:279-303, 2007. doi:10.1002/prot.21150
    3 Oct 2007 Firas Khatib Philip Bradley, David Baker.
    Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation.
    Proteins, Volume 65, Issue 4, Pages 922 - 929, 2006.
    http://www3.interscience.wiley.com/cgi-bin/abstract/113390048/ABSTRACT
    10 Oct 2007 John Archie Sepp Hochreiter, Martin Heusel, and Klaus Obermayer.
    Fast model-based protein homology detection without alignment
    Bioinformatics 2007 23: 1728-1736.
    doi:10.1093/bioinformatics/btm247
    17 Oct 2007 Josue Samayoa Dariusz Przybylski and Burkhard Rost.
    Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments
    Nucleic Acids Res. 2007 April; 35(7): 22382246.
    doi:10.1093/nar/gkm107
    24 Oct 2007 Martin MaderaAkhil P. Kamat, Arthur M. Lesk.
    Contact patterns between helices and strands of sheet define protein folding patterns. Proteins: Structure, Function, and Bioinformatics
    Volume 66, Issue 4, Pages 869-876
    doi:10.1002/prot.21241
    31 Oct 2007 George Shackelford Xin Gao, Dongbo Bu, Shuai Cheng Li, Ming Li, Jinbo Xu.
    Consensus Contact Prediction by Linear Programming.
    Proceedings LSS Computational Systems Bioinformatics Conference, 13-17 Aug 2007, UCSD. http://www.lifesciencessociety.org/CSB2007/toc/323.2007.html
    7 Nov 2007 Kevin Karplus recent results on peptide_plane rotation for secondary structure
    14 Nov 2007 Grant Thiltgen Kyoung-Jae Won, Thomas Hamelryck, AdamPrrügel-Bennett, and Anders Krogh
    An evolving method for learning HMM Structure: prediction of protein secondary structure.
    BMC Bioinformatics. 2007 Sep 21;8(1):357
    http://www.biomedcentral.com/1471-2105/8/357
    21 Nov 2007 John Kim Andrzej Kolinski and Dominik Gront.
    Comparative modeling without implicit sequence alignments.
    Bioinformatics 23: 2522-2527, (2007).
    http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/19/2522
    28 Nov 2007 Martin Paluszewski STRUCTURE CLUB Sinsheimer 123 12:30-1:40
    28 Nov 2007 Firas Khatib "Hbonds: is there anything they can't do? The key to solving the Pokefind dilemma"
    5 Dec 2007 Dietlind Gerloff Georg Neuberger, Georg Schneider and Frank Eisenhaber.
    pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model.
    Biology Direct 2007, 2:1
    http://www.biology-direct.com/content/2/1/1
    doi:10.1186/1745-6150-2-1
    12 Dec 2007 John Archie Optimizing model quality assessment to maximize tau

    Summer 2007 individual meeting schedule

    (Note: not on campus on Mondays and Wednesdays this summer.)

    time Tuesday Thursday Friday
    10:00
    10:30
    11:00 John Archie
    11:30
    12:00
    12:30
    1:00 Grant Thiltgen Martin Paluszewski
    1:30 Grant Thiltgen
    2:00 group meeting Firas Khatib
    2:30 group meeting
    3:00 group meeting
    3:30 Josue Samayoa
    4:00 George Shackelford bread and tea
    4:30 George Shackelford bread and tea
    5:00 bread and tea

    Summer 2007 Meeting times

    Lab meetings will be Thursdays 1:30-3 in     PSB 305 (the conference room).
    datespeakertopic/paper
    20 June 2007 Zack Sanborn using Rosetta Design
    28 June 2007 John Archie recent research on using predicted local structure in undertaker cost functions
    5 July 2007 Josue Samayoa recent research on short repeats
    12 July 2007 Kevin Karplus Better than Chance
    19 July 2007 no meeting Kevin at 3Dsig
    27 July 2007 no meeting Kevin at ISMB
    2 Aug 2007 Kevin, Dietlind ISMB recap
    9 Aug 2007 Martin Madera Rosetta developer's conference recap
    16 Aug 2007 Kevin Karplus Backrub operator and new n_ca_c cost funtion

    The Backrub Motion: How Protein Backbone Shrugs When a Sidechain Dances.
    Ian W. Davis, W. Bryan Arendall III, David C. Richardson and Jane S. Richardson.
    Structure, Volume 14, Issue 2, Pages 265-274, 2006
    doi:10.1016/j.str.2005.10.007

    Experimentally observed conformation-dependent geometry and hidden strain in proteins.
    P. Andrew Karplus.
    Protein Science, Vol 5, Issue 7, 1406-1420, 1996.
    http://www.proteinscience.org/cgi/content/abstract/5/7/1406

    also 16 Aug 2007 Martin Madera Andrew Leaver-Fay, Glenn L. Butterfoss, Jack Snoeyink, Brian Kuhlman.
    Proteins, Volume 28, Issue 8, Pages 1336-1341, 2007.
    http://www3.interscience.wiley.com/cgi-bin/abstract/114112024/ABSTRACT doi:10.1002/jcc.20626

    Scott M. Le Grand, Kenneth M. Merz Jr.
    Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables.
    Journal of Computational Chemistry 14(3):349-352, 1993.
    http://www3.interscience.wiley.com/cgi-bin/abstract/109582955/ABSTRACT doi:10.1002/jcc.540140309

    23 Aug 2007 no meeting? Kevin going to Tempest matinee
    30 Aug 2007 Thomas Juettemann research (improving protein-protein interaction information)
    6 Sept 2007 Joanna Sharman research

    Spring 2007 individual meeting schedule

    (Note: not on campus on Tuesdays.)

    time Monday Wednesday Thursday Friday
    10:00
    10:30 ugrad_curric?
    11:00 COT ugrad_curric? John Josue
    11:30 COT ugrad_curric? Firas
    12:00 COT BME 280B Firas
    12:30 MCD seminar Structure Club BME 280B MCD seminar
    1:00 MCD seminar Structure Club BME 280B MCD seminar
    1:30 MCD seminar MCD seminar
    2:00 BME220 BME220 Martin BME 220
    2:30 BME220 BME220 Martin BME 220
    3:00 Chris, Jon, Sylvia BME220 Hyunsung BME 220/BME fac
    3:30 Chris, Jon, Sylvia BME 281K BME fac
    4:00 office hoursBME 281K George bread and tea
    4:30 office hoursBME 281K bread and tea
    5:00 bread and tea

    Spring 2007 Meeting times

    Lab meetings will be Mondays Wednesdays 3:30-5 in     PSB 305 (the conference room).
    datespeakertopic/paper
    4 April 2007 George Shackelford Eyal E, Frenkel-Morgenstern M, Sobolev V, Pietrokovski S.
    A pair-to-pair amino acids substitution matrix and its applications for protein structure prediction.
    Proteins. 2007 Jan 22;67(1):142-153 doi:10.1002/prot.21223
    11 April 2007 Firas Khatib Peter Virnau, Leonid A. Mirny, Mehran Kardar.
    Intricate Knots in Proteins: Function and Evolution.
    PLoS Compututational Biology 2(9): e122
    doi:10.1371/journal.pcbi.0020122
    18 April 2007 Martin Madera Rodriguez, Abel and Schmidler, Scott. Combining sequence and structure information in protein alignments. (unpublished?, found on web at www.isds.duke.edu/~ar52/ISMB2006.pdf)
    25 April 2007 Josue Samayoa Zhang CASP7 paper
    preprint in /projects/compbio/papers/external/manu_review.pdf (not available on the web)
    2 May 2007 Dietlind Gerloff Qifang Xu , Adrian Canutescu, Zoran Obradovic and Roland L. Dunbrack, Jr
    ProtBuD: a database of biological unit structures of protein families and superfamilies.
    Bioinformatics 2006 22(23):2876-2882
    doi:10.1093/bioinformatics/btl490
    9 May 2007 Grant Thiltgen Practice talk on Hbond alphabets (for structure club next week)
    16 May 2007 Kevin Karplus Engineering proteinase K using machine learning and synthetic genes
    Jun Liao, Manfred K Warmuth, Sridhar Govindarajan, Jon E Ness, Rebecca P Wang, Claes Gustafsson and Jeremy Minshull
    BMC Biotechnology 2007,7:16
    doi:10.1186/1472-6750-7-16
    23 May 2007 Martin Madera new alignment tests, fold-recognition tests on profile-profile
    30 May 2007 George Shackelford Jianlin Cheng and Pierre Baldi.
    Improved residue contact prediction using support vector machines and a large feature set.
    BMC Bioinformatics. 2007; 8:113 Published online 2007 April 2.
    doi: 10.1186/1471-2105-8-113
    6 June 2007 Firas Khatib Chung-Jung Tsai, Jie Zheng, David Zanuy, Nurit Haspel, Haim Wolfson, Carlos Aleman, Ruth Nussinov.
    Principles of nanostructure design with protein building blocks.
    Proteins: Structure, Function, and Bioinformatics 68(1):1-12, 3 April 2007.
    doi:10.1002/prot.21413
    13 June 2007 Martin Madera COBALT: constraint-based alignment tool for multiple protein sequences.
    Jason S. Papadopoulos and Richa Agarwala/
    Bioinformatics 2007 23: 1073-1079.
    doi:10.1093/bioinformatics/btm076

    Richard E. Smith, Simon C. Lovell, David F. Burke, Rinaldo W. Montalvao, and Tom L. Blundell.
    Andante: reducing side-chain rotamer search space during comparative modeling using environment-specific substitution probabilities.
    Bioinformatics 2007 23: 1099-1105.
    doi:10.1093/bioinformatics/btm073

    Jan E. Gewehr, Volker Hintermair, and Ralf Zimmer.
    AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings.
    Bioinformatics 2007 23: 1203-1210.
    doi:10.1093/bioinformatics/btm089

    Winter 2007 Meeting times

    Lab meetings will be Mondays 3:30-5 in PSB 305 (the conference room).
    datespeakertopic/paper
    5 Jan 07 general discussion of upcoming conferences and of GDT, clens, and other model accuracy measures
    12 Jan 07Josue Improving the quality of protein structure models by selecting from alignment alternatives.
    Ingolf Sommer, Stefano Toppo, Oliver Sander, Thomas Lengauer and Silvio CE Tosatto
    BMC Bioinformatics 2006, 7:364
    doi:10.1186/1471-2105-7-364 http://www.biomedcentral.com/1471-2105/7/364
    15 Jan 07 no meeting: Martin Luther King Day
    22 Jan 07Martin Looger, LL and Hellinga, HW
    Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics.
    Journal of Molecular Biology, 307(1):429-445. 2001.
    doi:10.1006/jmbi.2000.4424
    29 Jan 07Ian Rickard WII controllers
    5 Feb 07Dietlind Selections from ECCB:

    Yanay Ofran and Burkhard Rost
    ISIS: interaction sites identified from sequence.
    Bioinformatics 2007 23(2):e13-e16;
    doi:10.1093/bioinformatics/btl303

    Iddo Friedberg, Tim Harder, Rachel Kolodny, Einat Sitbon, Zhanwen Li, Adam Godzik
    Using an alignment of fragment strings for comparing protein structures
    Bioinformatics 2007 23(2):e219-e224;
    doi:10.1093/bioinformatics/btl310

    9 Feb 07Ian Rickard WII controllers
    9 Feb 07 George Shackelford Canutescu,A.A., Shelenkov,A.A. and Dunbrack,R.L. (2003) A graph-theory algorithm for rapid protein side-chain prediction. Protein Science, 12, 2001-2014. http://www.proteinscience.org/cgi/content/abstract/12/9/2001
    16 Feb 07No meeting President's Day
    27 Feb 07John Archie Gianese G, Pascarella S.
    A Consensus Procedure Improving Solvent Accessibility Prediction
    J Comput Chem. 2006 Apr 15;27(5):621-6.
    doi:10.1002/jcc.20370
    5 Mar 07Kevin discuss BME 220 projects for next quarter
    12 Mar 07Grant Thiltgen Beeby M, O'Connor BD, Ryttersgaard C, Boutz DR, Perry LJ, Yeates TO
    The Genomics of Disulfide Bonding and Protein Stabilization in Thermophiles.
    PLoS Biology Vol. 3, No. 9, e309
    doi:10.1371/journal.pbio.0030309
    19 Mar 07Martin Madera Andreeva A, Murzin A.G
    Evolution of protein fold in the presence of functional constraints.
    Curr Opin Struct Biol. 2006 Jun;16(3):399-408
    26 Mar 07Break (no meeting)

    Winter 2007 individual meeting schedule

    time Monday Wednesday Thursday Friday
    9:30 COT
    10:00 COT
    10:30 COT/ugrad_curric
    11:00 ugrad_curric
    11:30 ugrad_curric George
    12:00 Josue BME 280B George
    12:30 Josue Structure Club BME 280B MCD seminar
    1:00 John Structure Club BME 280B MCD seminar
    1:30 John BME 280B MCD seminar
    2:00 Martin Grant Firas
    2:30 Martin Grant Firas
    3:00 BME fac
    3:30 BME 281Koffice hours BME fac
    4:00 BME 281Koffice hours bread and tea
    4:30 BME 281K bread and tea
    5:00 bread and tea

    Fall 2006 Meeting times

    Lab meetings will be Fridays 11am-12:20pm in PSB 305 (the new conference room), rather than the lab. Bread and tea will continue to be in the lab (PSB 313).
    datespeakertopic/paper
    22 Sept 06KarplusCASP7 analysis (GDT)
    29 Sept 06KarplusCASP7 analysis (real_hbonds)
    6 Oct 06Madera Zhang and Skolnick "Spicker: A clustering approach to identify near-native protein folds" Journal of Computational Chemistry 25(6):865-871, March 2004
    13 Oct 06Shackelford Douglas L. Theobald and Deborah S. Wuttke "THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures" Bioinformatics 2006 22(17):2171-2172. doi:10.1093/bioinformatics/btl332
    20 Oct 06Thiltgen Discussion of ways to select neural nets and learning protocols based on train-cross-train data (informal discussion)
    27 Oct 06Samayoa Physically realistic homology models built with ROSETTA can be more accurate than their templates
    Kira M. S. Misura, Dylan Chivian, Carol A. Rohl, David E. Kim, and David Baker
    PNAS April 4, 2006 vol. 103 no. 14 5361-5366 www.pnas.org/cgi/doi/10.1073/pnas.0509355103
    3 Nov 06Thiltgen Comparative Protein Modelling by Satisfaction of Spatial Restraints
    Andrej Šali and Tom L. Blundell
    Journal of Molecular Biology 234(3):779-815, 5 December 1993
    http://dx.doi.org/10.1006/jmbi.1993.1626
    (also copy in /projects/compbio/papers/external/Modeller-Sali-JMB93.pdf)
    10 Nov 06NO CLASS
    17 Nov 06George, Grant, Firas practice CASP and SAC-CASP talks
    24 Nov 06NO CLASS
    1 Dec 06SAC-CASP discuss alignment tests with Martin and John
    8 Dec 06Kevin plan Winter quarter---discuss CASP evaluations to do

    Fall 2006 individual meeting schedule

    time Monday Wednesday Thursday Friday
    10:00
    10:30
    11:00 BME281K
    11:30 BME281K
    12:00 BME 280B BME281K
    12:30 MCD seminar BME 280B MCD seminar
    1:00 MCD seminar BME 280B MCD seminar
    1:30 MCD seminar BME 280B MCD seminar
    2:00 BME 205 BME 205 BME 205
    2:30 BME 205 BME 205 BME 205
    3:00 BME 205 BME 205 BME 205
    3:30 office hours
    4:00 office hours BME 200 bread and tea
    4:30 BME 200 bread and tea
    5:00 BME 200 bread and tea
    5:30 BME 200

    Summer 2006 Meeting times

    CASP7 season started Monday 8 May 2006

    For summer 2006 we will have multiple weekly meetings:

    All lab meetings will take place in PSB 305 (the new conference room), rather than the lab. Bread and tea will continue to be in the lab.

    The lab meetings started at 2 during World Cup season, but are back to 1, now that the World Cup is over. (Exception, Wed tutorials remain at 2, since the SURFIT students have a conflict on Wednesdays.)

    Summer 2006 individual meeting schedule

    Individual project meetings have not been set yet. I will have individual meetings only for non-CASP projects (protein design, grant writing, advancement to candidacy, thesis research, ...).
    time Monday Wednesday Friday
    11:00Martin
    12:00 Josue
    1:00
    2:00CASP7 tutorial group
    3:00CASP7 tutorial group
    4:00 bread and tea

    Summer 2006 tutorials and science talks

    date person topic
    Wed 21 JunKhatib ProteinShop
    Fri 23 JunMadera intro to nanotubes
    Wed 28 JunKarplus interpreting the results of the automatic prediction
    Fri 30 JunKarplus scoring H-bonds without hydrogens
    Wed 5 JulKarplus basic process for optimizing a comparative model, creating a dimer
    Fri 7 Jul no meeting
    Wed 12 JulKarplus strategies for dealing with ab initio targets
    Fri 14 JulSanborn protein design example
    Wed 19 JulKarplus undertaker conformation-change operators
    Fri 21 JulKarplus target meeting
    Wed 26 Jul no meeting (Karplus family vacation)
    Fri 28 Jul no meeting (Karplus family vacation)
    Mon 31 JulKhatib knot finding (practice for ISMB) +target meeting
    Wed 2 Aug no meeting ISMB
    Fri 4 Aug no meeting ISMB
    Wed 9 Aug no meeting ISMB
    Fri 11 Aug no meeting ISMB
    Wed 16 Aug Karplus ?
    Fri 18 Aug no meeting (BINF curriculum, Stanford)
    Wed 23 Aug Karplus ?
    Fri 25 Aug Madera profile-profile alignment

    Spring 2006 individual meeting schedule

    time Thursday Friday
    10:00
    11:00 Martin George
    12:00 280B
    1:00 280B Firas
    2:00 Josue lab group
    3:00 Grant
    4:00 Navya and Erichbread&tea

    Spring 2006, group meeting activities

    For Spring 2006, we are meeting Fridays at 2 pm in Baskin 310 until we move to PSB (last meeting in Baskin on April 28). Thereafter we will meet in PSB 313 (still Fridays at 2).

    For Spring 2006, we are meeting 2-3 in Baskin 310 Physical Sciences Building (PSB) 313 on Fridays.

    datespeakertopic/paper
    7 April 2006everyoneplanning for quarter
    14 April 2006Greg Dougherty ProteinShop+undertaker interface
    21 April 2006everyonescheduling CASP training and journal club
    28 April 2006Kevin Karplus interpreting automatic prediction and using undertaker to change prediction
    5 May 2006NONE GRAD SYMPOSIUM no lab meeting
    12 May 2006Martin Madera highlights of nanotech conference (also start CASP7 target discussions)
    19 May 2006CASP7 target discussion
    26 May 2006Firas Khatib (Karplus at UCLA)
    2 June 2006CASP7 target discussion
    9 June 2006CASP7 target discussionProgress reports due
    16 June 2006CASP7 target discussion

    Winter 2006 individual meeting schedule, including BME220 students

    time Monday Wednesday Thursday Friday
    10:30-11 Donald Chau set up bread
    11-11:30 Pinal KanabarJosue Samayoa
    11:30-12 Tim Sterne-WeilerJosue SamayoaSuma Potluri
    12-12:30 281K Guillaume Jospin
    12:30-1Mark MitchellRoger Chen 281K George Shackelford
    1-1:30Mark Mitchell Grant ThiltgenGeorge Shackelford
    1:30-2travel travel travel
    2-2:30220 220 280B 220
    2:30-3220 220 280B 220
    3-3:30220+travel 220+travel 220+travel
    3:30-4Greg DoughertyZack SanbornFiras KhatibChris Wong
    4-4:30open office Zack SanbornFiras KhatibBread and tea
    4:30-5open office Miriam BellowsGibron KuryBread and tea
    5-5:30 Yuta Komai

    Winter 2006, group meeting activities

    For Winter 2006, we are meeting 12-1 in Baskin 310 on Thursdays.
    datespeakertopic/paper
    3 Jan 2006everyonestatus update
    12 Jan 2006Introductions, Scheduling for quarter
    19 Jan 2006Josue Samayoa Gong Cheng, Bin Qian, Ram Samudrala, and David Baker. Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Research 33(18):5861-5867, 2005. doi:10.1093/nar/gki894
    26 Jan 2006Grant Thiltgen Olver Sander, Ingolf Sommer, Thomas Lengauer. Local protein structure prediction using discriminatrive models. BMC Bioinformatics 7:14, 2006. doi:10.1186/1471-2105-7-14
    2 Feb 2006Firas Khatib Yarov-Yarovoy V, Schonbrun J, Baker D. Multipass membrane protein structure prediction using Rosetta. Proteins. 2005
    9 Feb 2006(status reports)
    16 Feb 2006Mark Mitchell Melissa Cline, Kevin Karplus, Richard Lathrop, Temple Smith, Robert G. Rogers Jr., and David Haussler. Information-theoretic dissection of pairwise contact potentials. Proteins: Structure, Function, and Genetics, 49(1):7-14, 1 October 2002.

    Since the paper is short, I will supplement my presentation with a proof of the statement on p.10:
    "Theory shows that for a sufficiently large sample size, both statistics nÎ(X,Y) and T(X,Y) have approximately the same distribution"

    23 Feb 2006George Shackelford Riedmiller, M. and Braun, H. A direct adaptive method for faster backpropagation learning: the RPROP algorithm. IEEE International Conference on Neural Networks. 1:586-591, 28 March-1 April 1993. doi:10.1109/ICNN.1993.298623
    2 Mar 2006Zack Sanborn Carleton L. Kingsford , Bernard Chazelle and Mona Singh. Solving and analyzing side-chain positioning problems using linear and integer programming Bioinformatics 21:1028-1039, 2005.
    9 Mar 2006??? not scheduled yet
    16 Mar 2006??? not scheduled yet
    23 Mar 2006exam week (status reports)

    Fall 2005 individual meeting schedule

    Monday Thursday Friday
    11:15-12:15 Josue11:15-12:15 George
    1:30-2:30 Grant
    2:30-3:30 Firas

    Fall 2005, group meeting activities

    datespeakertopic/paper
    28 Sept 2005everyonebrief summer update
    5 Oct 2005Firas journal club: Bradley et al., Toward High-Resolution de Novo Structure Prediction for Small Proteins, Science 2005 309: 1868-1871
    (Oops, I forgot to keep a record this quarter!)

    Summer 2005, group meeting activities

    datespeakertopic/paper
    6 July 2005Kevin Karplusultimate library
    13 July 2005Oscar HurHMM for TIM barrels
    20 July 2005George Shackelford Detecting coevolving amino acid sites using Bayesian mutational mapping. Matthew W. Dimmic, Melissa J. Hubisz, Carlos D. Bustamante, and Rasmus Nielsen. Bioinformatics 2005 21(suppl_1):i126-i135
    27 July 2005Kevin Karplusneural nets for predicting local structure and designing proteins
    3 Aug 2005Josue Samayoaintro to Rosetta and highlights of Rosetta developer's conference

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