UCSC BME 220 Spring 2007 schedule

UCSC BME 220 Schedule

Protein Bioinformatics, Spring 2007

(Last Update: 15:08 PDT, 4 June 2007 )

Date	Person	Topic
Apr 4	Karplus	Administrivia, review of protein structure
Apr 6	Karplus	Project list
Apr 9	Gerloff	Overview of experimental techniques & efforts for determining protein (3-D) structure: (i) X-ray Crystallography Lecture slides etc: Framing Lecture Slides (Dietlind) Iain McNae's protein X-ray crystallography slides Amplitude versus phase (illustration) Link of the week: http://www.usm.maine.edu/~rhodes/GRHomePage.html: Gale Rhodes's Home page. Of particular interest for us are Judging the Quality of Macromolecular Models , and Chapter 8 in his book "Crystallography Made Crystal Clear" (Academic Press) - scanned in for you here, though it does look nicer in the book [Note: This relates to Monday's lecture but is not required before class]
Apr 11	Gerloff	Structure Determination: (ii) NMR; (iii) cryo-EM [extremely briefly] Structural Genomics Lecture slides etc: Framing Lecture Slides (Dietlind) Janice Bramham's protein NMR slides Wave nature of electrons (relevant to EM) Structural Genomics Overview (Stats) and Centers Berkeley Structural Genomics Center
Apr 13	Gerloff	Discussion: Quality? (check out Gerd Kleywegt's tutorial on model validation) PDB format and the RCSB/PDB resource famous/interesting examples of protein structures is it determination or modeling (low-resolution structure examples) etc [Note: more pointers still to be added]
Apr 16	Karplus	Interpreting output of SAM-Txx prediction protocol: Blast output, multiple sequence alignments, sequence logos.
Apr 18	Karplus	Interpreting output of SAM-Txx prediction protocol: secondary structure predictions, consensus prediction, burial definition.
Apr 20	Martin Paluszewski	Lattice-based prediction using deterministic search (tabu search and branch-and-bound) and contact numbers
Apr 23	Gerloff	Descriptive and/or derived information about protein 3-D structures Historical (biologist) ways to describe a protein 3-D structure. Overview of standard information derived from new structures - how does this compare to the "developer's view" that we adopted last week? Link of the week: http://www.ebi.ac.uk/pdbsum : PDBsum Lecture slides: Lecture Slides (Dietlind)
Apr 25	Gerloff	DNA-Day! Brief intro to Homework 2, then public outreach event at Bay Tree Conference Center
Apr 27	Gerloff	Discussion: challenges in this area examples of inaccurate derived information etc
May 7	Karplus	Steps of SAM-T06 prediction, iterated search, local structure prediction, what single-domain hits look like, damage done by undertaker to good alignment. Uses PF13_0036 and PF13_0036 S100-L190 as examples.
May 9	Karplus	Meaning of undertaker cost functions, using S100-L190 try2.costfcn as outline. Also discussed Lennard-Jones potential and backbone-dependent rotamer libraries (which undertaker does not currently use).
May 11	Karplus	Use of decoy sets for testing cost functions (better-than-real and Kendall's tau) constraints in undertaker, Hbond geometry---scoring hbonds without explicit hydrogens.
May 14	Karplus	undertaker "cheating" cost functions: rmsd, rmsd-ca, GDT, smooth GDT, clens
May 16	Karplus	Hbond cheating cost functions, undertaker commands: try1.under
May 18	Karplus	undertaker conformation generation
May 21	Gerloff	pet peeves about writing, intro to continuous assessment (EVA and LiveBench)
May 23	Gerloff
May 25	Gerloff
May 30	Marcos Woehrmann	Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402, 1997.
May 30	Chris Szeto	Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M. Crystal structure of rhodopsin: A G protein-coupled receptor. Science 289, 739-745, 2005. doi:10.1126/science.289.5480.739
Jun 1	Dan Sam	Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A 89, 10915-10919, 1992.
Jun 1	Jonathan Magasin	Karlin S, Altschul SF. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci U S A 87, 2264-2268, 1990.
Jun 4	John Archie	Henikoff S, Henikoff JG. Position-based sequence weights. J Mol Biol 243, 574-578, 1994. doi:10.1016/0022-2836(94)90032-9
Jun 4	Shyamini Vasili	Andrew M. Davis, Simon J. Teague, and Gerard J. Kleywegt. Application and Limitations of X-ray Crystallographic Data in Structure-Based Ligand and Drug Design. Angewandte Chemie International Edition 2003, 42: 2718--2736. doi:10.1002/anie.200200539
Jun 6	Eric Scott	Jeffrey PD, Russo AA, Polyak K, Gibbs E, Hurwitz J, Massague J, Pavletich NP. Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex. Nature 376, 313-320, 1995. doi:10.1038/376313a0
Jun 6	John Kim	Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science 302, 1364-1368, 2003. doi:10.1126/science.1089427
Jun 8	Sylvia Do	Bower MJ, Cohen FE, Dunbrack RL Jr. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol 267, 1268-1282, 1997. doi:10.1006/jmbi.1997.0926
Jun 8	Murat Iskar	Horita DA, Baldisseri DM, Zhang W, Altieri AS, Smithgall TE, Gmeiner WH, Byrd RA. Solution structure of the human Hck SH3 domain and identification of its ligand binding site. J Mol Biol 278, 253-265, 1998. doi:10.1006/jmbi.1998.1690
Jun 12	Posters 4--7

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BS, MS, and PhD programs

Karplus's lab page

UCSC Bioinformatics research

Questions about page content should be directed to

Kevin Karplus
Biomolecular Engineering
University of California, Santa Cruz
Santa Cruz, CA 95064
USA
karplus@soe.ucsc.edu
1-831-459-4250