Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models.

ABSTRACT: We propose a novel method of calculation of free energy for coarse grained models of proteins by combining our newly developed multibody potentials with entropies computed from elastic network models of proteins. Multi-body potentials have been of much interest recently because they take into account three dimensional interactions related to residue packing and capture the cooperativity of these interactions in protein structures. Combining four-body non-sequential, four-body sequential and pairwise short range potentials with optimized weights for each term, our coarse-grained potential improved recognition of native structure among misfolded decoys, outperforming all other contact potentials for CASP8 decoy sets and performance comparable to the fully atomic empirical DFIRE potentials. B

SUBMITTER: Zimmermann MT 

PROVIDER: S-EPMC3227679 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature