Optimization of the GBMV2 implicit solvent force field for accurate simulation of protein conformational equilibria.

ABSTRACT: Accurate treatment of solvent environment is critical for reliable simulations of protein conformational equilibria. Implicit treatment of solvation, such as using the generalized Born (GB) class of models arguably provides an optimal balance between computational efficiency and physical accuracy. Yet, GB models are frequently plagued by a tendency to generate overly compact structures. The physical origins of this drawback are relatively well understood, and the key to a balanced implicit solvent protein force field is careful optimization of physical parameters to achieve a sufficient level of cancellation of errors. The latter has been hampered by the difficulty of generating converged conformational ensembles of non-trivial model proteins using the popular replica exchange sampling tec

SUBMITTER: Lee KH 

PROVIDER: S-EPMC5407932 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature