DARS (Decoys As the Reference State) potentials for protein-protein docking.

ABSTRACT: Decoys As the Reference State (DARS) is a simple and natural approach to the construction of structure-based intermolecular potentials. The idea is generating a large set of docked conformations with good shape complementarity but without accounting for atom types, and using the frequency of interactions extracted from these decoys as the reference state. In principle, the resulting potential is ideal for finding near-native conformations among structures obtained by docking, and can be combined with other energy terms to be used directly in docking calculations. We investigated the performance of various DARS versions for docking enzyme-inhibitor, antigen-antibody, and other type of complexes. For enzyme-inhibitor pairs, DARS provides both excellent discrimination and docking results, eve

SUBMITTER: Chuang GY 

PROVIDER: S-EPMC2567923 | biostudies-literature | 2008 Nov

REPOSITORIES: biostudies-literature