OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing.

ABSTRACT: Here we report an orientation-dependent statistical all-atom potential derived from side-chain packing, named OPUS-PSP. It features a basis set of 19 rigid-body blocks extracted from the chemical structures of all 20 amino acid residues. The potential is generated from the orientation-specific packing statistics of pairs of those blocks in a non-redundant structural database. The purpose of such an approach is to capture the essential elements of orientation dependence in molecular packing interactions. Tests of OPUS-PSP on commonly used decoy sets demonstrate that it significantly outperforms most of the existing knowledge-based potentials in terms of both its ability to recognize native structures and consistency in achieving high Z-scores across decoy sets. As OPUS-PSP excludes interact

SUBMITTER: Lu M 

PROVIDER: S-EPMC2669442 | biostudies-literature | 2008 Feb

REPOSITORIES: biostudies-literature