Comparing Bound and Unbound Protein Structures Using Energy Calculation and Rotamer Statistics

Issue title: This is the special Issue The German Conference on Bioinformatics 2001, 7-10 October, Braunschweig, Germany

Article type: Research Article

Authors: Koch, Kerstin | Zöllner, Frank | Neumann, Steffen | Kummert, Franz | Sagerer, Gerhard

Affiliations: Technische Fakultät, AG Angewandte Informatik, Universität Bielefeld, Postfach 100131, 33501 Bielefeld, Germany

Note: [] E-mail: [email protected]

Note: [] E-mail: [email protected]

Note: [] E-mail: [email protected]

Note: [] E-mail: [email protected]

Note: [] E-mail: [email protected]

Abstract: Protein data in the PDB covers only a snapshot of a protein structure. For flexible docking confor-mational changes need to be considered. Rotamer statistics provide the likelihood for side chain conformations, and further comparison of bound and unbound state yields differences in preferred positions. Furthermore, we do a full sampling of selected angles and apply the AMBER force field. Conformation of energy minima complies with the rotamer statistics. Both types of information target the reduction of search space for enumerative docking algo-rithms and provide parameters for elastic docking.

Keywords: Rotamer library, flexible protein-protein docking, energy calculations, AMBER force field, side chain flexibility, flexibility measure

Journal: In Silico Biology, vol. 2, no. 3, pp. 351-368, 2002