BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations.

ABSTRACT: Quantifying protein-ligand binding has attracted the attention of both theorists and experimentalists for decades. Many methods for estimating binding free energies in silico have been reported in recent years. Proper use of the proposed strategies requires, however, adequate knowledge of the protein-ligand complex, the mathematical background for deriving the underlying theory, and time for setting up the simulations, bookkeeping, and postprocessing. Here, to minimize human intervention, we propose a toolkit aimed at facilitating the accurate estimation of standard binding free energies using a geometrical route, coined the binding free-energy estimator (BFEE), and introduced it as a plug-in of the popular visualization program VMD. Benefitting from recent developments in new collective v

SUBMITTER: Fu H 

PROVIDER: S-EPMC5869121 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature