Jan. 3, 2003

Publications in Computational Chemistry on Molecular Docking, Flexibility, Conformation, etc., by :

Bajaj, C et al. :
- A Geometric Approach to Molecular Docking and Similarity, 1994.
Canny, J. et al. :
- Geometric problems in molecular biology and robotics, 1994.
Kavraki, L.E. et al. :
- A Dimensionality Reduction Approach to Modeling Protein Flexibility, 2002.
- Molecular Docking: A Problem with Thousands of Degrees of Freedom, 2001.

BibTeX references.

"A central question for the docking problem is how to represent the geometry of the cavity, an how to compare it to the geometry of the ligand." (Kavraki)

Conformation: unique 3D shape of a molecule which corresponds to a global minimum of its total energy, specified only by the chemical composition of the molecule (e.g., consider the problem of protein folding).

Web links:

Strategic Simulation Initiative: Computational Structural Biology:
http://cbcg.lbl.gov/ssi-csb/

A Geometric Approach to Molecular Docking and Similarity

C. Bajaj, F. Bernardini & K. Sugihara
Technical Report CSD-TR-94-017, CS, Purdue U., March 1994.

Geometric problems in molecular biology and robotics

Parsons, D. and J. Canny
Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology.
Stanford, August 1994.

A Dimensionality Reduction Approach to Modeling Protein Flexibility

M. Teodoro, G.N. Phillips, Jr., and L. Kavraki
Proceedings of the ACM International Conference on Research in Computational Biology (RECOMB),
pp. 299-308, ACM Press, April 2002.

Molecular Docking: A Problem with Thousands of Degrees of Freedom

M. Teodoro, G.N. Phillips, Jr., and L. Kavraki
IEEE International Conference on Robotics and Automation (ICRA), Seoul, Korea, pp.960-900, 2001.

Web-link : http://www.cs.rice.edu/CS/Robotics/publications.html

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