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.
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.
Komatsu
Katsuichiro
K
School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan.
Kurihara
Youji
Y
Iwadate
Mitsuo
M
Takeda-Shitaka
Mayuko
M
Umeyama
Hideaki
H
D001554:Benzene / Q000737:chemistry; D001665:Binding Sites; D016000:Cluster Analysis; D057927:Hydrophobic and Hydrophilic Interactions; D046911:Macromolecular Substances; D008958:Models, Molecular; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012997:Solvents / Q000737:chemistry
D046911:Macromolecular Substances; D011506:Proteins; D012997:Solvents; D001554:Benzene