Exploring the Effectiveness of Binding Free Energy Calculations

Increasing the accuracy of the evaluation of ligand-binding energies is one of the most important tasks of current computational biology. Here we explore the accuracy of free energy perturbation (FEP) approaches by comparing the performance of a “regular” FEP method to the one using replica exchange to enhance the sampling on a well-defined benchmark. The examination was limited to the so-called alchemical perturbations which are restricted to a fragment of the drug, and therefore, the calculation is a relative one rather than the absolute binding energy of the drug. Overall, our calculations reach the 1 kcal/mol accuracy limit. It is also shown that the accurate prediction of the position of water molecules around the binding pocket is important for FEP calculations. Interestingly, the replica exchange method does not significantly improve the accuracy of binding energies, suggesting that we reach the limit where the force field quality is a critical factor for accurate calculations.