| date | topic | papers to read (see below) |
| 29 March | logisitics and overview of topics for quarter | |
| 31 March | bond angles and torsion angles (how to compute), rotamers, rotamer library, undertaker's 9-d Gaussian mixture used in place of rotamer library, intro to rigid transforms | |
| 5 April | quaternions and rigid transformations | |
| 7 April | Guest Lecture: Marshall Bern (PARC) Fun with mass spec | |
| 12 April (first) | Grant Thiltgen: Protein blocks | http://www.ebgm.jussieu.fr/~debrevern/PBs/ There are several papers on protein blocks and we should read at least the first one: Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks A.G. de Brevern, C. Etchebest, and S. Hazout. Proteins: Structure, Function and Genetics (2000), 41:271-287. PDF from author's website |
| 12 April (second) | Nathan Bahr:evaluation of local structure | Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry Rachel Karchin, Melissa Cline, Yael Mandel-Gutfreund, and Kevin Karplus. Proteins: Structure, Function, and Genetics (2003) 51(4):504-514. preprint from authors' website |
| 14 April | Kevin away | |
| 19 April (first) | Ron Chao: DALI | Protein Structure Comparison by Alignment of Distance Matrices Liisa Holm and Chris Sander. Journal of Molecular Biology (1993) 233:123-138. |
| 19 April (second) | Wing Wong: VAST | Surprising similarities in structure comparison J. Gilbrat, T. Madej, and S. Bryant. Current Opinion in Structural Biology (1996) 6:377-385. |
| 21 April | Project Proposal due | |
| 21 April (first) | Alex Williams: FATCAT | Database searching by flexible protein structure alignment Yuzhen Ye and Adam Godzik. Protein Science (2004), 13:1841-1850. |
| 21 April (second) | Tim Dreszer: contact maps | Recovery of protein structure from contact maps M. Vendruscolo, E. Kussell, and E. Domany. Folding and Design (1997) 2:295-306. |
| 26 April | Homework 1 due | |
| 26 April (first) | David Ng: Rosetta | Assembly of Protein Tertiary Structures from Fragments with Similar Local Sequences Using Simulated Annealing and {Bayesian} Scoring Functions Kim T. Simons, Charles Kooperberg, Enoch Huang, and David Baker. Journal of Molecular Biology (1997) 268:209-225. |
| 26 April (second) | Craig Lowe: TOP7 | Design of a novel globular protein fold with atomic-level accuracy. Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Science. 2003 Nov 21;302(5649):1364-1368. PMID: 14631033 |
| 28 April (first) | Courtney Onodera: Psipred | Protein secondary structure prediction based on position-specific scoring matrices D.T. Jones. Journal of Molecular Biology (1999) 292:195-202. |
| 28 April (second) | Sol Katzman: predict-2nd program | draft of paper |
| 3 May (first) | Lam Vu: SAM-Txx |
casp4 casp5 casp6 |
| 3 May (second) | Kevin Karplus: protein design by backpropagation (proposal) | |
| 5 May (first) | Nathan Bahr: MUSCLE multiple aligner | Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97 |
| 5 May (second) | Kevin Karplus: undertaker | |
| 10 May (first) | Jes Frellsen: TOPS |
D. Gilbert, D. Westhead, and J. Viksna (2003). Techniques for comparison, pattern matching and pattern discovery: From sequences to protein topology, in "Artificial Intelligence and Heuristic Methods in Bioinformatics", Paolo Frasconi and Ron Shamir (Eds), IOS Press, ISBN 1-58603-294-1, pp 128-147. (PDF) (some material from) Pattern matching and pattern discovery algorithms for protein topologies Juris Viksna and David Gilbert. Algorithms in Bioinformatics: First International Workshop, WABI 2001 Proceedings, LNCS 2149 pp 98-111, ISBN 3-540-42516-0, (pre-publication version) |
| 10 May (second) | Ron Chao: FFAS | Comparison of sequence profiles. Strategies for structural predictions using sequence information. Rychlewski, L., Jaroszewski, L., Li, W. & Godzik, A. Protein Science (2000), 9:232-241. |
| 12 May (first) | Sol Katzman: Hellinga's protein design | Computational design of receptors for an organophosphate surrogate of the nerve agent soman Malin Allert, Shahir S. Rizk, Loren L. Looger, and Homme W. Hellinga PNAS 2004 101: 7907-7912 |
| 12 May (second) | Craig Lowe: Skolnick and Zhang | Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Zhang Y, Skolnick J. Biophysics Journal 2004 Oct;87(4):2647-55. |
| 17 May (first) | Courtney Onodera: folding rates |
The topomer search model: A simple, quantitative theory
of two-state protein folding kinetics
Dmitrii Makarov and Kevin Plaxco.
Protein Science (2003), 12:17-26.
Using Protein Folding Rates to Test Protein Folding Theories Blake Gillespie and Kevin Plaxco. Annu. Rev. Biochem. (2004), 73:837-839. |
| 17 May (second) | David Ng: force fields |
Empirical Force Fields for Biological
Macromolecules: Overview and Issues.
A.D. MacKerell, Jr.
Journal of Computational
Chemistry, 2004 Oct;25(13):1584-604.
PMID: 15264253
Force Fields for Protein Simulation, Jay W. Ponder and David A. Case, Advances in Protein Chemistry, 2003;66:27-85. PMID: 14631816. Energy functions for protein design, D. Benjamin Gordon, Shannon A. Marshall, and Stephen L. Mayo, Current Opinion in Structural Biology, 1999, 9:509-513. PMID: 10449371. GROMACS User Manual, Version 3.2,
|
| 19 May (first) | Grant Thiltgen: hydrogen bonds | The Hydrogen Bond in the Solid State Thomas Steiner. Angewandte Chemie (International ed. in English) 2002, 41(1), 49-76. |
| 19 May (second) | Tim Dreszer: decoy sets | Protein Decoy Sets for Evaluating Energy Functions Gilis, Dimitri. Journal of Biomolecular Structure and Dynamics ISSN 0739-1102. 21(6):725-854. 2004. |
| 24 May | Progress report due | |
| 24 May (first) | Alex Williams: directed evolution of proteins |
Totally In Vitro Protein Selection Using mRNA-Protein
Fusions and Ribosome Display.
Richard W. Roberts.
Current Opinion in Chemical Biology,
3, 268-273
(1999).
Phage Display Smith G.P. and Petrenko V.A. Chemical Reviews, V. 97, N2, p. 391-410 (1997). |
| 24 May (second) | Lam Vu: unfolding pathways | "New view" of protein folding reconciled with the old through multiple unfolding simulations. Lazaridis T, Karplus M. Science. 1997 Dec 12;278(5345):1928-31. |
| 26 May |
Class canceled on vote of students. Students interested in poster design should attend Karplus lab meeting at 1:00pm on WED 25 May. | |
| 31 May | Jes Frellsen: 1d-to-3d | Recoverable one-dimensional encoding of three-dimensional protein structures Akira R. Kinjo and Ken Nishikawa Bioinformatics 2005 21: 2167-2170. |
| 2 June | Grad Research Symposium 11-1 Graduate Student Commons | |
| 2 June | Undergrad Research Symposium 2-4 Thimann Courtyard | |
| 7 June | Poster Session 4-7 p.m. CANCELLED |
Registration is required as soon as possible for both events. See http://graddiv.ucsc.edu/gradsymposium.html for information about the graduate research symposium. Deadline for registration is Monday May 16.
Applications for the undergraduate one are available to pick up at the School of Engineering Undergraduate Advising Office and are due by April 15th.