Optimal clustering for detecting near-native conformations in protein docking.

ABSTRACT: Clustering is one of the most powerful tools in computational biology. The conventional wisdom is that events that occur in clusters are probably not random. In protein docking, the underlying principle is that clustering occurs because long-range electrostatic and/or desolvation forces steer the proteins to a low free-energy attractor at the binding region. Something similar occurs in the docking of small molecules, although in this case shorter-range van der Waals forces play a more critical role. Based on the above, we have developed two different clustering strategies to predict docked conformations based on the clustering properties of a uniform sampling of low free-energy protein-protein and protein-small molecule complexes. We report on significant improvements in the automated pred

SUBMITTER: Kozakov D 

PROVIDER: S-EPMC1366636 | biostudies-literature | 2005 Aug

REPOSITORIES: biostudies-literature