The Jarzynski binding free energy can effectively rank ligand-protein affinities in inadequate samplings

The use of the Jarzynski equality for estimating ligand–protein binding free energies are illustrated for cases of inadequate samplings. Data obtained from a large amount (104) of work are thus converged to an incorrect value, due to creation of a distorted Gaussian-like distribution. However, even in such cases, the Jarzynski equality can effectively rank binding affinities in the early stage of rational drug design. A combination of steered molecular dynamics calculations, Jarzynski relation and block averaging can provide such relative binding free energies having significantly better correlations in the cases of the thrombin and HIV-1 complexes examined.