These authors contributed equally to this work.
Searching for protein–protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues
Article first published online: 24 JUN 2005
Copyright © 2005 Wiley-Liss, Inc.
Proteins: Structure, Function, and Bioinformatics
Special Issue: Second Meeting on the Critical Assessment of PRedicted Interactions
Volume 60, Issue 2, pages 289–295, 1 August 2005
How to Cite
Terashi, G., Takeda-Shitaka, M., Takaya, D., Komatsu, K. and Umeyama, H. (2005), Searching for protein–protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues. Proteins, 60: 289–295. doi: 10.1002/prot.20572
- Issue published online: 24 JUN 2005
- Article first published online: 24 JUN 2005
- Manuscript Accepted: 3 MAR 2005
- Manuscript Received: 14 JAN 2005
- Grant-in-Aid for Scientific Research on Priority Areas (C) “Genome Information Science” from the Ministry of Education, Culture, Sports, Science, and Technology of Japan
- protein–protein docking;
- protein-binding site;
- hydrophobic interaction;
- benzene cluster;
- induced fit problem;
- interaction site prediction;
In CAPRI Rounds 1 and 2, we assumed that because there are many ionic charges that weaken electrostatic interaction forces in living cells, the hydrophobic interaction force might be important entropically. As a result of Rounds 1 and 2, the predictions for binding sites and geometric centers were acceptable, but those of the binding axes were poor, because only the largest benzene cluster was used for generating the initial docking structures. These were generated by fitting of benzene clusters formed on the surface of receptor and ligand. In CAPRI Rounds 3–5, the grid-scoring sum on the protein–protein interaction surface and the pairwise potential of the amino acid residues, which were indicated as coming easily into the protein–protein interaction regions, were used as the calculation methods, along with the smaller benzene clusters that participated in benzene cluster fitting. Good predicted models were obtained for Targets 11 and 12. When the modeled receptor proteins were superimposed on the experimental structures, the smallest ligand root-mean-square deviation (RMSD) values corresponding to the RMSD between the model and experimental structures were 6.2 Å and 7.3 Å, respectively. Proteins 2005;60:289–295. © 2005 Wiley-Liss, Inc.