Workshop in Bioinformatics

Fall Semester 2002-2003 (semester 'a')

Instructor: Max Shatsky
e-mail:maxshats at
Phone : (03) 640-5395

Office Hours: by an appointment

This is a third year workshop in Computer Science.

The subject of the workshop is Structural Bioinformatics, which tackles 3D problems in the field of Molecular Biology, using techniques developed in the fields of Computer-Vision and Robotics.
No prior knowledge in Biology is assumed or required.

Dates (all dates are subject to change):
24-28 Nov 2002: Design submission.
12-16 Jan 2003: Project submission.

Lectures (PowerPoint):
Lecture 1
Lecture 2
Lecture 3
Lecture 4

Previous Workshop (year 2001)
Previous Workshop (year 2000)
GAMB++ (or directly The GAMB library Documentation.)
Educational Resources
PDB (Protein Data Bank)
SCOP (Structural Classification of Proteins)

Project: Your task is to implement a program that performs a protein docking. This is a project for ALL groups. At the end of the workshop your programs will be evaluated. Three works that give the best results will receive a bonus to a final grade. Despite that a subject of the project is common to all groups, every group should implement a different algorithm. Your own ideas are welcome and even more preferable to the methods described in the articles. In other words, the goal is to perform a protein docking applying all your skills and imagination!!!
Groups are 3-4 students. If you can't find a group please e-mail me.
You are welcome to use the GAMB++ library (link below). Actually, most of the work is already done, you need only to locate suitable classes. And read FAQ at the bottom of this page.

Projects (some changes in the project definitions are possible):

Docking Overview
* Principles of docking: An overview of search algorithms and a guide to scoring functions. Inbal Halperin, Buyong Ma, Haim Wolfson, Ruth Nussinov Proteins 2002, vol 47, p409-443
Docking (based on Geometric Hashing)

* From Computer Vision to Protein Structure and Association, Paper in PS. H.J. Wolfson and R. Nussinov,
   In ``Computational Methods in Molecular Biology" (S. Salzberg, D.B. Searls, S. Kasif, eds.), Elsevier Science B.V., Chapter 14, 313-334 (1998).
* Small Molecule Recognition: Solid Angles Surface representation and Molecular Shape Complementarity,Paper in PS.R. Norel, H.J. Wolfson and R. Nussinov, Combinatorial Chemistry & High Throughput Screening, 2, 177-191, (1999).
* Efficient Unbound Docking of Rigid Molecules. Paper in PDF Duhovny, D. and Nussinov, R. and Wolfson, H.J. Workshop on Algorithms in Bioinformatics (WABI'02), Springer Verlag,2002.
Docking (based on Quadratic Shape Descriptors)
 * Goldman BB, Wipke WT. QSD quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock).Proteins. 2000 Jan 1;38(1):79-94.
 *  Goldman BB, Wipke WT. Quadratic Shape Descriptors. 1. Rapid Superposition of Dissimilar Molecules Using Geometrically Invariant Surface Descriptors.J.
    Chem. Inf. Comput. Sci., 40 (3), 644 -658, 2000. (paper)

Additional Papers.


Q: Where is GAMB++ library?
A: Enter one of a Unix machines. The path to the library is: /home/silly6/mol/lib/egamb++/. On Linux use liblinuxoptgamb++.a (or liblinuxdebgamb++.a for debuging with compiling option "-g")

Q: I want to see some example using GAMB++ library.
A: Almost every class has its own example code. But here is a simple program.

Q: Where is a program that creates a molecule surface?
A: There are two such programs. See /home/silly6/mol/software/CP/SurfacePointsLinux/README.

Q: What software is available for visualization of molecule structures?
A: Rasmol is a freeware visualization program available for download. On Unix it is installed at /home/silly6/mol/utils/Rasmol/ (Linux only).

Q: GAMB++ library for Windows?
A: One of the students managed to convert GAMB++ library to Windows. Here is his remarks. Here is converted code. Notice, there will be no update for this code (25-Dec 2001).