Structural Bioinformatics
Spring Semester 2002/2003
Graduate Course, Computer Science Department
TelAviv University.
Table of Contents:

Instructor:
Prof. Haim
Wolfson

email: wolfson@tau.ac.il
TA: Max Shatsky

email: maxshats at tau.ac.il
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, 232254, (1999)
Overview:
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,
receptorligand docking and, if time permits, protein folding.
Since proteins are 3dimensional geometric objects, efficient algorithms
which handle such objects can be of great benefit for the solution of these
'reallife' 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 3D protein structure
(for Computer Science students) and present stateoftheart 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.
SOME TOPICS THAT WILL BE DISCUSSED :

3D Protein matching

3D (molecular) Surface Representation

Extraction of Geometrical and Biological (3D Motion) invariant indices.

ReceptorLigand Docking (resembles a solution of 3D puzzle)

Matching and Docking of Flexible 3D structures.

Protein Folding
Perquisites ;
The course is targeted for M.Sc. and 3^{rd}
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 email wolfson@cs.tau.ac.il
or via telephone: 6406476
Recommended Web Sites:

rcsb Internet Courses on the Principles of Protein Structure.

Weizmann
Institute Genome and Bioinformatics Home Page.
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