Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction.

ABSTRACT: Incorporation of effective backbone sampling into protein simulation and design is an important step in increasing the accuracy of computational protein modeling. Recent analysis of high-resolution crystal structures has suggested a new model, termed backrub, to describe localized, hinge-like alternative backbone and side-chain conformations observed in the crystal lattice. The model involves internal backbone rotations about axes between C-alpha atoms. Based on this observation, we have implemented a backrub-inspired sampling method in the Rosetta structure prediction and design program. We evaluate this model of backbone flexibility using three different tests. First, we show that Rosetta backrub simulations recapitulate the correlation between backbone and side-chain conformations in th

SUBMITTER: Smith CA 

PROVIDER: S-EPMC2603262 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature