GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction.

ABSTRACT: An accurate scoring function is a key component for successful protein structure prediction. To address this important unsolved problem, we develop a generalized orientation and distance-dependent all-atom statistical potential. The new statistical potential, generalized orientation-dependent all-atom potential (GOAP), depends on the relative orientation of the planes associated with each heavy atom in interacting pairs. GOAP is a generalization of previous orientation-dependent potentials that consider only representative atoms or blocks of side-chain or polar atoms. GOAP is decomposed into distance- and angle-dependent contributions. The DFIRE distance-scaled finite ideal gas reference state is employed for the distance-dependent component of GOAP. GOAP was tested on 11 commonly used dec

SUBMITTER: Zhou H 

PROVIDER: S-EPMC3192975 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature