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Evaluation of the third solvent clusters fitting procedure for the prediction of protein–protein interactions based on the results at the CAPRI blind docking study
Author(s) -
Komatsu Katsuichiro,
Kurihara Youji,
Iwadate Mitsuo,
TakedaShitaka Mayuko,
Umeyama Hideaki
Publication year - 2003
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10385
Subject(s) - solvent , benzene , cluster (spacecraft) , docking (animal) , biological system , chemistry , computational chemistry , binding energy , computer science , chemical physics , physics , biology , organic chemistry , atomic physics , medicine , nursing , programming language
To predict protein–protein interactions, rough or coarse handling for the induced fit problem is proposed. Our method involves the overlap of two hydrophobic interactions as “third solvent clusters fitting.” Predictions for binding sites and geometric centers were acceptable, but those of the binding axes were poor. In this study, only the largest benzene cluster was used for the third solvent clusters fitting. For the next CAPRI targets, we must perform protein–protein interaction analyses, which include other smaller benzene clusters. Proteins 2003;52:15–18. © 2003 Wiley‐Liss, Inc.