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Keywords:

  • protein–protein docking;
  • protein-binding site;
  • hydrophobic interaction;
  • benzene cluster;
  • induced fit problem

Abstract

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.