Princeton CS Dept |
COS597A, Fall 2005
|
This course provides an introduction to structural bioinformatics, focusing on geometric analysis of three-dimensional protein structures. It starts with a review of protein fundamentals and then quickly moves into computational techniques for analyzing protein structures. Example topics include binding site detection, small molecule docking, and structure-based function prediction. The class meetings comprise a mix of lectures and presentations of recent papers, and the coursework includes readings, presentations in class, and a course project. The course is open to undergraduates and graduate students from all departments and fields.
The course meets on Mondays and Wednesdays at 1:30-2:50PM in room 402 of the
Computer Science Building.
Final project presentations will be in room CS 402 at 2PM on
Thursday, January 26, 2006.
| Date | Topic | Guest Speaker | Book | Papers | Slides | Readings |
| Mon 9/19 | Course introduction | Ch 1 | html | [Goldsmith-Fischman03] | ||
| Wed 9/21 | Protein structure fundamentals | Josh Zees, Julie (Yu) Chen | Ch 2 | html | pdf1, pdf2 | [Birbeck96] |
| Mon 9/26 | Protein function prediction | Ch 19 | html | [Watson05] [Wild04] | ||
| Wed 9/28 | Protein structure alignment | Ch 16 | html | [Sierk04] [Krissinel04] [Brown96] | ||
| Mon 10/3 | Binding site detection (geometry) | Josh Podolak | - | html | [Laskowski96a] [Liang98c] [An05] | |
| Wed 10/5 | Binding site detection (evolution & chemistry) | html | [Campbell03] [Bartlett02] [Laurie05] | |||
| Mon 10/10 | Binding site matching (points) | Phil Shilane, Szymon Rusinkiewicz | - | html | [Schmitt02] [Shulman-Peleg04] | |
| Wed 10/12 | Binding site matching (points) | Helen Berman | - | html | [Berman00] | |
| Mon 10/17 | Binding site matching (surfaces) | - | html | [Hofbauer04] | ||
| Wed 10/19 | Project proposals | All Students | - | html | - | |
| Mon 10/24 | Binding site matching (volumes) | - | html | [Kastenholz00] [Katchalski-Katzir92] | ||
| Wed 10/26 | Binding site matching (templates) | - | html | [Jones04] [Wallace97] | ||
| BREAK | ||||||
| Mon 11/7 | Protein-ligand docking (scoring and search) | Megan Pomianek | Ch 22 | html | [Taylor02b] [Gohlke02] [Halperin02] [Friesner04] [Rarey96] [Jones97] [Ewing01] |
|
| Wed 11/9 | Protein-ligand docking (evaluation) | - | html | [Kellenberger04] [Kotoyianni04] [Perola04] [Cole05] | ||
| Mon 11/14 | Drug screening | Bill Welsh | Ch 23 | html | [Lengauer04] [Lyne02] [Zauhar03] | |
| Wed 11/16 | Project presentations | All Students | - | html | - | |
| Mon 11/21 | Drug design I | Joe Corkery | Ch 22 | html | [Marrone97] | |
| Wed 11/23 | Drug design II | Jermont Chen | - | html | [Klebe00] | |
| Mon 11/28 | Protein-protein docking | Ch 20 | html | [Smith02] [Szilagyi05] [Janin05] [Wodak04] | ||
| Mon 12/5 | Structure determination I | Ch 24-26 | html | [Floudas06] | ||
| Wed 12/7 | Structure determination II (x-ray crystallography) | Fred Hughson | Ch 4 | html | ||
| Mon 12/12 | Structure determination III | Scott McAllister | Ch 27 | html | ||
| Wed 12/14 | Project presentations | All Students | - | html | - | |
