Minimal ensembles of side chain conformers for modeling protein-protein interactions.

ABSTRACT: The goal of this article is to reduce the complexity of the side chain search within docking problems. We apply six methods of generating side chain conformers to unbound protein structures and determine their ability of obtaining the bound conformation in small ensembles of conformers. Methods are evaluated in terms of the positions of side chain end groups. Results for 68 protein complexes yield two important observations. First, the end-group positions change less than 1 Å on association for over 60% of interface side chains. Thus, the unbound protein structure carries substantial information about the side chains in the bound state, and the inclusion of the unbound conformation into the ensemble of conformers is very beneficial. Second, considering each surface side chain separately in

SUBMITTER: Beglov D 

PROVIDER: S-EPMC3297704 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature