Computations of standard binding free energies with molecular dynamics simulations.

ABSTRACT: An increasing number of studies have reported computations of the standard (absolute) binding free energy of small ligands to proteins using molecular dynamics (MD) simulations and explicit solvent molecules that are in good agreement with experiments. This encouraging progress suggests that physics-based approaches hold the promise of making important contributions to the process of drug discovery and optimization in the near future. Two types of approaches are principally used to compute binding free energies with MD simulations. The most widely known is the alchemical double decoupling method, in which the interaction of the ligand with its surroundings are progressively switched off. It is also possible to use a potential of mean force (PMF) method, in which the ligand is physically se

SUBMITTER: Deng Y 

PROVIDER: S-EPMC3837708 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature