Proceedings of the Korean Society for Bioinformatics Conference (한국생물정보학회:학술대회논문집)
- 2005.09a
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- Pages.294-299
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- 2005
Unbound Protein-Protein Docking Using Conformational Space Annealing
- Lee, Kyoung-Rim (School of Computational Sciences, Korea Institute for Advanced Study) ;
- Joo, Kee-Hyoung (School of Computational Sciences, Korea Institute for Advanced Study) ;
- Lee, Joo-Young (School of Computational Sciences, Korea Institute for Advanced Study)
- Published : 2005.09.22
Abstract
We have studied unbound docking for 12 protein-protein complexes using conformational space annealing (CSA) combined along with statistical pair potentials. The CSA, a powerful global optimization tool, is used to search the conformational space represented by a translational vector and three Euler amgles between two proteins. The energy function consists of three statistical pair-wise energy terms; one from the distance-scaled finite ideal-gas reference state (DFIRE) approach by Zhou and the other two derived from residue-residue contacts. The residue-residue contact terms describe both attractive and repulsive interactions between two residues in contact. The performance of the CSA docking is compared with that of ZDOCK, a well-established protein-protein docking method. The results show that the application of CSA to the protein-protein docking is quite successful, indicating that the CSA combined with a good scoring function is a promising method for the study of protein-protein interaction.
Keywords