Free energies of ligand binding for structurally diverse compounds.

ABSTRACT: The one-step perturbation approach is an efficient means to calculate many relative free energies from a common reference compound. Combining lessons learned in previous studies, an application of the method is presented that allows for the calculation of relative binding free energies for structurally rather diverse compounds from only a few simulations. Based on the well known statistical-mechanical perturbation formula, the results do not require any empirical parameters, or training sets, only limited knowledge of the binding characteristics of the ligands suffices to design appropriate reference compounds. Depending on the choice of reference compound, relative free energies of binding rigid ligands to the ligand-binding domain of the estrogen receptor can be obtained that show good a

SUBMITTER: Oostenbrink C 

PROVIDER: S-EPMC1100734 | biostudies-literature | 2005 May

REPOSITORIES: biostudies-literature