 Bar Ilan University Faculty of Medicine |
81-871, Spring 2012
|
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 exercises. The course is open to graduate students from all faculties.
The course meets on Mondays at 8:00-10:00AM in room 209 of the Faculty of Medicine.
Schedule
| Date | Topic | Book | Other | Slides | Project | Readings |
| Monday 5/3 | Course introduction | Ch 1 | Course books | ppt | Goldsmith-Fischman (2003) | |
| Monday 12/3 | Structure Fundamentals: Protein and nucleic acids | Ch 2-3 | Pymol | ppt | Assignment 1 (Solution) | Branden-Tooze (1999) |
| Monday 19/3 | Structure representation and coordinate formats | Ch 9-11 | PDB | ppt | Assignment 2 (Solution) | Berman (2003) |
| Monday 26/3 | Structure determination using NMR, crystallography, and cryoEM | Ch 4-6 | CNS | ppt | Assignment 3 (Solution) | |
| Monday 2/4 | No Class (Pessach vacation) | |||||
| Monday 9/4 | No Class (Pessach vacation) | |||||
| Monday 16/4 | No Class | |||||
| Monday 23/4 | Structure databases and classification | Ch 12, 17-18 | SCOP | CATH | ppt | Assignment 4 (Solution) | Kolodny (2006) |
| Monday 30/4 | Calculation of secondary structure and solvent exposure | Ch 19 | DSSP | STRIDE | ppt | Assignment 5 (Solution) | Kabsch-Sander (1983) |
| Monday 7/5 | Prediction of secondary structure, membrane region, and solvent exposure | Ch29 | PSIPRED | ppt | Assignment 6 (Solution) | |
| Monday 14/5 | Structure prediction: Homology modeling | Ch 30-31 | PyMod | ppt | Assignment 7 (Solution) | Sali-Blundell(1993) |
| Monday 21/5 | Structure prediction: Ab-initio modeling | Ch 32 | ROBETTA | ppt | Assignment 8 | |
| Monday 28/5 | No Class (Shavuot vacation) | |||||
| Monday 4/6 | Motion prediction: Normal modes and molecular dynamics | Ch 37 | ElNemo | GROMACS | ppt | Assignment 9 | (Solution) | Lindahl(2001) Suhre(2004) |
| Monday 11/6 | Prediction of binding site and docking | Ch 27 | GRAMM | ppt | Assignment 10| (Solution) | |
| Monday 18/6 | Computer aided drug design | Ch 34 | Patchdock | 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
- Maya Amitay
- Genadiy Fonar
- Yitav Glantz
- Noa Maatuk
- Faiga Mazgal