Old schedules for Karplus bioinformatics lab
UC Santa Cruz

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