SymmRef: a flexible refinement method for symmetric multimers.

ABSTRACT: Symmetric protein complexes are abundant in the living cell. Predicting their atomic structure can shed light on the mechanism of many important biological processes. Symmetric docking methods aim to predict the structure of these complexes given the unbound structure of a single monomer, or its model. Symmetry constraints reduce the search-space of these methods and make the prediction easier compared to asymmetric protein-protein docking. However, the challenge of modeling the conformational changes that the monomer might undergo is a major obstacle. In this article, we present SymmRef, a novel method for refinement and reranking of symmetric docking solutions. The method models backbone and side-chain movements and optimizes the rigid-body orientations of the monomers. The backbone move

SUBMITTER: Mashiach-Farkash E 

PROVIDER: S-EPMC3155011 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature