Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization.

ABSTRACT: Most protein structural prediction algorithms assemble structures as reduced models that represent amino acids by a reduced number of atoms to speed up the conformational search. Building accurate full-atom models from these reduced models is a necessary step toward a detailed function analysis. However, it is difficult to ensure that the atomic models retain the desired global topology while maintaining a sound local atomic geometry because the reduced models often have unphysical local distortions. To address this issue, we developed a new program, called ModRefiner, to construct and refine protein structures from Cα traces based on a two-step, atomic-level energy minimization. The main-chain structures are first constructed from initial Cα traces and the side-chain rotamers are then ref

SUBMITTER: Xu D 

PROVIDER: S-EPMC3218324 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature