Bar Ilan University
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Structural BioinformaticsInstructor: Dr. Avraham SamsonTutors: Dr. Naama Bloch, Amichai Liberman81-871, Fall 2019 |
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 10 assignments.
The course meets on Mondays at 16:00-18:00 at the Faculty of Medicine, in room 102 for lectures, and in room 211 for hand-on assignments.
Schedule
| Date | Topic | Software | Slides | Assignment |
| Monday 28/10 | Course introduction | ppt | ||
| Monday 04/11 | Structure Fundamentals: Protein and nucleic acids | Pymol | ppt | Assignment 1 |
| Monday 11/11 | Structure representation and coordinate formats | PDB | ppt | Assignment 2 |
| Monday 18/11 | Structure determination using NMR, crystallography, and cryoEM | CNS | ppt | Assignment 3 |
| Monday 25/11 | Structure databases and classification | SCOP | CATH | ppt | Assignment 4 |
| Monday 02/12 | Calculation of secondary structure and solvent exposure | DSSP | STRIDE | ppt | Assignment 5 |
| Monday 09/12 | Prediction of secondary structure, membrane region, and solvent exposure | PSIPRED | ppt | Assignment 6 |
| Monday 16/12 | Structure prediction: Homology modeling | PyMod | ppt | Assignment 7 |
| Monday 23/12 | Structure prediction: Ab-initio modeling | ROBETTA | I-TASSER | ppt | Assignment 8 |
| Monday 30/12 | No Class (Hanuka vacation) | |||
| Monday 06/01 | Motion prediction: Normal modes and molecular dynamics | ElNemo | GROMACS | ppt | Assignment 9 |
| Monday 13/01 | Prediction of binding site and docking | GRAMM | Patchdock | ppt | Assignment 10 |
| Monday 20/01 | Computer aided drug design | Dockblaster | ppt | Assignment 11 |
Related Courses
- Michael Levitt
Structural Biology Dept.
Stanford University
"Structural Biology 228"
- Thomas Funkhouser
Molecular Biophysics and Biochemistry
Princeton University
"Structural Bioinformatics"
Coursework
- Course books
- P.E. Bourne, H. Weissig, Structural Bioinformatics, Wiley-Liss, Hoboken, NJ, 2003. This is a good introductory book on structural bioinformatics. It practical rather than theoretical - it reviews the main sources of structural data (e.g., PDB, NDB, etc.) and surveys the most popular methods used for predicting structure, aligning structures, predicting function, etc.
- C.A. Orengo, D.T. Jones, J.M. Thornton,
Bioinformatics: Genes, Proteins, & Computers, BIOS Scientific Publishers, Abingdon, UK, 2004. This is a good book on bioinformatics, with particular emphasis on structural bioinformatics.
- Class Participation
- Attend for your own benefit.
- Contribute ideas during all class discussions
- Course Project
- At the end of each class there will be an assignment to be submitted by the beginning of next class
- Each assignment is worth 10 points in the final grade. If you submit 11 assignment, then only 10 with the highest grade will be used for the final grade.
Enrolled Students
- Balqees Kadry
- Maysa Aborya
- Mirwat Jiris
- Samar Gani
- Sagi Hamo
- Wessal Hanut
- Almog Levy
- Rosa Levin
- Lelyan Moadi
- Bisan Salah
- Yasmin Suaed