Structural Bioinformatics


Spring Semester 2002/2003
Graduate Course, Computer Science Department  Tel-Aviv University.

Table of Contents:

Instructor: Prof. Haim Wolfson

TA: Max Shatsky

e-mail: maxshats at

Lectures and assignments:

Lecture 1   Assignment 1

Lecture 2   TA 2   Assignment 2

Lecture 3   Assignment 3

Lecture 4a   Lecture 4b  

Lecture 5   Assignment 4

Quadratic Shape Descriptors (QSD)  

Largest Common Subtrees and Largest Common Point Sets


Project References:

1.Wolfson, H. J., Generalizing the Generalized Hough Transform, Pattern Recognition Letters, vol. 12(9), pp. 565 - 573, (1991).

2. G. Verbitsky, R. Nussinov, H.J. Wolfson, Structural Comparison Allowing Hinge Bending, Swiveling Motions, PROTEINS, 34, 232-254, (1999)




In the course we shall discuss geometric algorithms which assist in the solution of major problems in Protein Structure analysis. We shall concentrate on algorithmic research for protein structural comparison, receptor-ligand docking and, if time permits, protein folding.

Since proteins are 3-dimensional geometric objects, efficient algorithms which handle such objects can be of great benefit for the solution of these 'real-life' problems. In this sense there is much in common to the problems occurring in protein analysis and drug design with central problems in Computer Vision or Computational Geometry. The course will highlight these ideas and concentrate on algorithms which originated in Computer Vision/Computational Geometry research. Special emphasis will be given to the practical solution of the problems at hand.

We shall shortly introduce some basic knowledge on 3-D protein structure (for Computer Science students) and present state-of-the-art geometric algorithms which tackle the above mentioned problems. Many of the algorithms, which will be presented at the course, were developed at Tel Aviv University by the Computational Structural Biology group under the supervision of Prof. Ruth Nussinov from the Molecular Medicine Institute and Prof. Haim Wolfson from the Computer Science Department.


Perquisites ;

The course is targeted for M.Sc. and 3rd year B.Sc students of Computer Science. Students of other departments (e.g. Chemistry, Biology, Medicine) may participate if they have enough mathematical and computational maturity. No knowledge of Molecular Biology is assumed.
  • Formal Prerequisites: Can be found on the "Idion". Students who don't have the formal prerequisites and want to register should approach Prof. Haim Wolfson via e-mail or via telephone: 640-6476

  • Recommended Web Sites:
    1. rcsb Internet Courses on the Principles of Protein Structure.
    2. Weizmann Institute Genome and Bioinformatics Home Page.
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