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.
Lectures (Power Point):
PDB (Protein Data Bank)
SCOP (Structural Classification of Proteins)
GAMB++ (or directly The GAMB library Documentation.)
Possible projects (some changes in the project definitions are possible):
Link to the relevant papers (though, not all of them)
1. Pairwise Structural Alignment (based on Geometric Hashing)
2. Pairwise Structural Alignment (based on Geometric Hashing)
4. Flexible Pairwise Structural Alignment (FlexProt algorithm)
* FleProt paper
* FlexProt web site
5. 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):79-94.6. Docking (based on Geometric Hashing)
* 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)
* R. Norel, H.J. Wolfson and R. Nussinov, Small Molecule Recognition: Solid Angles Surface representation and Molecular Shape Complementarity,
Combinatorial Chemistry & High Throughput Screening, 2, 177-191, (1999).
* R. Norel, D. Petrey, H.J. Wolfson and R. Nussinov,
Examination of Shape Complementarity in Docking of Unbound Proteins, text, pdf,
PROTEINS, 36, 307-317, (1999).
* H.J. Wolfson and R. Nussinov,
From Computer Vision to Protein Structure and Association, text (including figures and tables),
In ``Computational Methods in Molecular Biology" (S. Salzberg, D.B. Searls, S. Kasif, eds.), Elsevier Science B.V., Chapter 14,
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).