An Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials.

ABSTRACT: Gay-Berne anisotropic potential has been widely used to evaluate the non-bonded interactions between coarse-grained particles being described as elliptical rigid bodies. In this paper, we are presenting a coarse-grained model for twenty kinds of amino acids and proteins, based on the anisotropic Gay-Berne and point electric multipole (EMP) potentials. We demonstrate that the anisotropic coarse-grained model, namely GBEMP model, is able to reproduce many key features observed from experimental protein structures (Dunbrack Library) as well as from atomistic force field simulations (using AMOEBA, AMBER and CHARMM force fields) while saving the computational cost by a factor of about 10~200 depending on specific cases and atomistic models. More importantly, unlike other coarse-grained approach

SUBMITTER: Shen H 

PROVIDER: S-EPMC3958967 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature