The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities.

ABSTRACT: The Binding Energy Distribution Analysis Method (BEDAM) for the computation of receptor-ligand standard binding free energies with implicit solvation is presented. The method is based on a well established statistical mechanics theory of molecular association. It is shown that, in the context of implicit solvation, the theory is homologous to the test particle method of solvation thermodynamics with the solute-solvent potential represented by the effective binding energy of the protein-ligand complex. Accordingly, in BEDAM the binding constant is computed by means of a weighted integral of the probability distribution of the binding energy obtained in the canonical ensemble in which the ligand is positioned in the binding site but the receptor and the ligand interact only with the solvent

SUBMITTER: Gallicchio E 

PROVIDER: S-EPMC2992355 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature