Approaches To Protein-Ligand Binding From Computer Simulations

Accurate computation of protein-ligand binding affinities is a challenging goal with great potential value in the design of therapeutic agents. Applications of statistical mechanics simulations to the problem are considered that feature full atomic-level descriptions of the protein, ligand and aqueous environment. Basic concepts on the methodology and intermolecular interactions in solution are presented along with results of Monte Carlo simulations for binding of inhibitors by trypsin and thrombin.