Workshop in Bioinformatics (0368.3500.03)

Fall Semester 2001-2002

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):
Lecture 1
Lecture 2,3
Lecture 4
Lecture 5

Links:
Educational Resources
PDB (Protein Data Bank)
SCOP (Structural Classification of Proteins)
GAMB++ (or directly The GAMB library Documentation.)
Previous workshop
 

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)

+ Point Alignment (Ca and Cb)
+Vector Alignment (Ca->Cb)
+ Optimal Grid Distribution
*  Bachar O, Fischer D, Nussinov R, Wolfson H. A computer vision based technique for 3-D sequence-independent structural comparison of proteins. Protein Eng. 1993 Apr;6(3):279-88.

2. Pairwise Structural Alignment (based on Geometric Hashing)

+ Point Alignment (Cb and Amino Acid centroids)
+ Geometric + Amino Acid Matching Score
* Bachar O, Fischer D, Nussinov R, Wolfson H. A computer vision based technique for 3-D sequence-independent structural comparison of proteins. Protein Eng. 1993 Apr;6(3):279-88.
 
 
3. Flexible Pairwise Structural Alignment (based on Geometric Hashing)
 
* G. Verbitsky, R. Nussinov, H.J. Wolfson,
   Structural Comparison Allowing Hinge Bending, Swiveling Motions, text, pdf,
   PROTEINS, 34, 232-254, (1999).
* R. Nussinov, H.J. Wolfson,
   Efficient Computational Algorithms for Docking and for Generating and Matching a Library of Epitopes I. Rigid and Flexible
   Docking Algorithms, text,
   Combinatorial Chemistry & High Throughput Screening, 2, 277-287, (1999).
   http://www.math.tau.ac.il/~wolfson/on-line-articles.html

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.
    (paper)
 *  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)
 

6. Docking (based on Geometric Hashing)

* 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,
   313-334 (1998).
  http://www.math.tau.ac.il/~wolfson/on-line-articles.html

FAQ:

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).