Free Energy Calculations in Biological Systems. How Useful Are They in Practice?

Applications of molecular simulations targeted at the estimation of free energies are reviewed, with a glimpse into their promising future. The methodological milestones paving the road of free energy calculations are summarized, in particular free energy perturbation and thermodynamic integration, in the framework of constrained or unconstrained molecular dynamics. The continuing difficulties encountered when attempting to obtain accurate estimates are discussed with an emphasis on the usefulness of large–scale numerical simulations in non–academic environments, like the world of the pharmaceutical industry. Applications of the free energy arsenal of methods is illustrated through a variety of biologically relevant problems, among which the prediction of protein–ligand binding constants, the determination of membrane–water partition coefficients of small, pharmacologically active compounds — in connection with the blood–brain barrier, the folding of a short hydrophobic peptide, and the association of transmembrane α–helical domains, in line with the “two– stage” model of membrane protein folding. Current strategies for improving the reliability of free energy calculations, while making them somewhat more affordable, and, therefore, more compatible with the constraints of an industrial environment, are outlined.