Princeton CS Dept |
COS597A, Fall 2007
|
This course provides an introduction to structural bioinformatics, focusing on geometric analysis of three-dimensional protein and other macromolecular 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, folding, 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 two half-semester course projects. The course is open to undergraduates and graduate students from all departments and fields.
| Date | Topic | Speaker | Slides | Book | Papers | Bibliography |
| Tues Sep 18 | Course introduction | Ch 1 | [Goldsmith-Fischman03] | html | ||
| Thur Sep 20 | Protein structure fundamentals | Hui-Wen Shih | pdf1, pdf2 | Ch 2, 3 | [Birbeck96] | html |
| Tues Sep 25 | Protein structure determination | Fred Hughson | Ch 4-6 | html | ||
| Thur Sep 27 | Protein structure analysis | Meghan Bellows | Ch 7, 12-15 | html | ||
| Tues Oct 2 | Protein binding site analysis | Ch 19-21 | [Bartlett02] [Nayal06] | html | ||
| Thur Oct 4 | Protein binding site detection I | [Laskowski96a] [Liang98c] [An05] | html | |||
| Tues Oct 9 | Protein binding site detection II | Alan Barnes | [Bagley95a] [Rossi06] | html | ||
| Thur Oct 11 | Protein structure alignment | Pete DiMaggio | pdf1, pdf2 | Ch 16 | [Sierk04] [Krissinel04] [Brown96] | html |
| Tues Oct 16 | Protein binding site matching I | [Schmitt02] [Shulman-Peleg04] | html | |||
| Thur Oct 18 | Protein binding site matching II | [Hofbauer04] | html | |||
| Tues Oct 23 | Protein binding site matching III | [Kastenholz00] [Katchalski-Katzir92] | html | |||
| Thur Oct 25 | Project presentations | |||||
| BREAK | ||||||
| Thur Nov 6 | Protein-ligand docking I | Ch 22 |
[Taylor02b]
[Gohlke02]
[Halperin02]
[Friesner04] |
html | ||
| Thurs Nov 8 | Protein-ligand docking II | Zach Devito | [Kellenberger04] [Wang04] [Marsden04] | html | ||
| Tues Nov 13 | Virtual screening | Bill Welsh | Ch 23 | [Lengauer04] [Lyne02] [Zauhar03] | html | |
| Thurs Nov 15 | Protein-protein docking | Matt Naylor | [Smith02] [Szilagyi05] [Janin05] [Wodak04] | html | ||
| Tues Nov 20 | Drug design | Joe Corkery | html | |||
| Thur Nov 22 | Thanksgiving | |||||
| Tues Nov 27 | Protein structure prediction I | Peng Jiang | Ch 24 | [Floudas06] | html | |
| Thur Nov 29 | Protein structure prediction II | Ashwin Subramani | Ch 27 | html | ||
| Tues Dec 4 | Protein structure prediction III | Roland Dunbrack | Ch 25-26 | html | ||
| Thur Dec 6 | Protein design I | Alejandro Ochoa | html | |||
| Tues Dec 11 | Protein design II | Joanna Slusky | html | |||
| Thur Dec 13 | No class | html | ||||
| Mon Dec 17 | Project presentations | |||||
| Tues Jan 15 | Final presentations |