computational study for protein-protein docking using global optimization and empirical potentials计算研究蛋白质对接使用全局优化和经验势.pdf

Int. J. Mol. Sci. 2008, 9, 65-77 International Journal of Molecular Sciences ISSN 1422-0067 © 2008 by MDPI /ijms/ Full Research Paper Computational Study for Protein-Protein Docking Using Global Optimization and Empirical Potentials Kyoungrim Lee Department of Bioinformatics and Life Science, Soongsil University, 1-1 Sangdo5-dong, Dongjak-gu Seoul 156-743, Korea; E-mail: krlee@ssu.ac.kr Received: 2 December 2007 / Accepted: 15 January 2008 / Published: 22 January 2008 Abstract: Protein-protein interactions are important for biochemical processes in biological systems. The 3D structure of the macromolecular complex resulting from the protein- protein association is a very useful source to understand its specific functions. This work focuses on computational study for protein-protein docking, where the individually crystallized structures of interacting proteins are treated as rigid, and the conformational space generated by the two interacting proteins is explored extensively. The energy function consists of intermolecular electrostatic potential, desolvation free energy represented by empirical contact potential, and simple repulsive energy terms. The conformational space is six dimensional, represented by translational vectors and rotational angles formed between two interacting proteins. The conformational sampling is carried out by th