 Bar Ilan University Faculty of Medicine |
81-871, Spring 2014
|
Description
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 hands-on software trials, and the coursework includes readings, and home assignments.
The course meets on Thursdays at 8:00-10:00AM in room 102 of the Faculty of Medicine.
Schedule
| Date | Topic | Book | Other | Slides | Project | Readings |
| Thursday 27/02 | Course introduction | Ch 1 | Course books | ppt | Goldsmith-Fischman (2003) | |
| Thursday 06/03 | Structure Fundamentals: Protein and nucleic acids | Ch 2-3 | Pymol | ppt | Assignment 1 | Branden-Tooze (1999) |
| Thursday 13/03 | No class (Purim vacation) | |||||
| Thursday 20/03 | Structure representation and coordinate formats | Ch 9-11 | PDB | ppt | Assignment 2 | Berman (2003) |
| Thursday 27/03 | Structure determination using NMR, crystallography, and cryoEM | Ch 4-6 | CNS | ppt | Assignment 3 | |
| Thursday 03/04 | Structure databases and classification | Ch 12, 17-18 | SCOP | CATH | ppt | Assignment 4 | Kolodny (2006) |
| Thursday 10/04 | No Class (Pessach vacation) | |||||
| Thursday 17/04 | No Class (Pessach vacation) | |||||
| Thursday 23/04 | No Class (Pessach vacation) | |||||
| Thursday 30/04 | Calculation of secondary structure and solvent exposure | Ch 19 | DSSP | STRIDE | ppt | Assignment 5 | Kabsch-Sander (1983) |
| Thursday 08/05 | Prediction of secondary structure, membrane region, and solvent exposure | Ch29 | PSIPRED | ppt | Assignment 6 | |
| Thursday 15/05 | Structure prediction: Homology modeling | Ch 30-31 | PyMod | ppt | Assignment 7 | Sali-Blundell(1993) |
| Thursday 22/05 | Structure prediction: Ab-initio modeling | Ch 32 | ROBETTA | I-TASSER | ppt | Assignment 8 | |
| Thursday 29/05 | Motion prediction: Normal modes and molecular dynamics | Ch 37 | ElNemo | GROMACS | ppt | Assignment 9 | Lindahl(2001) Suhre(2004) |
| Thursday 04/06 | No Class (Shavuot vacation) | |||||
| Thursday 12/06 | Prediction of binding site and docking | Ch 27 | GRAMM | Patchdock | ppt | Assignment 10 | |
| Thursday 19/06 | Computer aided drug design | Ch 34 | Dockblaster | ppt | Assignment 11 | Schneidman-Duhovny (2005) |
Related Courses
- Michael Levitt
Structural Biology Dept.
Stanford University
"Structural Biology 228"
- Thomas Funhauser
Molecular Biophysics and Biochemistry
Princeton University
"Structural Bioinformatics"
Coursework
- Reading
- P.E. Bourne, H. Weissig, Structural Bioinformatics, Wiley-Liss, Hoboken, NJ, 2003.
- Read assigned paper(s) for each lecture
- Class Participation
- Attend for your own benefit.
- Contribute ideas during all class discussions
- Course Project
- At the end of each class there will be a home exercise to be submitted by the beginning of next class
- Each excercise is worth 10 points in the final grade. If you submit 11 exercises, then only 10 with the highest grade will be used for the final grade
Students
- Faculty of Medicine
- Yoav Bahat
- Meirav Baydani
- Alexandra Boginia
- Mark Lumkin
- Ilya Mistetsky
- Ola Orgil
- Amir Shechvitz
- Karin Shemer
- Efrat Shuster
- Chen Tor