Standard binding free energies from computer simulations: What is the best strategy?

ABSTRACT: Accurate prediction of standard binding free energies describing protein:ligand association remains a daunting computational endeavor. This challenge is rooted to a large extent in the considerable changes in conformational, translational and rotational entropies underlying the binding process that atomistic simulations cannot easily capture. In spite of significant methodological advances, reflected in a continuously improving agreement with experiment, a characterization of alternate strategies aimed at measuring binding affinities, notably their respective advantages and drawbacks, is somewhat lacking. Here, two distinct avenues to determine the standard binding free energy are compared in the case of a short, proline-rich peptide associating to the Src homology domain 3 of tyrosine kin

SUBMITTER: Gumbart JC 

PROVIDER: S-EPMC3685508 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature