Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates.

ABSTRACT: We introduce a novel method called restrain-free energy perturbation-release (R-FEP-R) to estimate conformational free energy changes via an alchemical path, which for some conformational landscapes like those associated with cellular signaling proteins in the kinase family is more direct and readily converged than the corresponding free energy changes along the physical path. The R-FEP-R method was developed from the dual topology free energy perturbation method that is widely applied to estimate the binding free energy difference between two ligands. In R-FEP-R, the free energy change between two conformational basins is calculated by free energy perturbations that remove those atoms involved in the conformational change from their initial conformational basin while simultaneously growin

SUBMITTER: He P 

PROVIDER: S-EPMC6092130 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature