“…7-10 Currently, a wide range of alchemical free energy methods provides the most robust and accurate estimates of binding affinities from molecular dynamics simulations. 3,7,11-15 These methods include Thermodynamic Integration (TI) 11,16-18 and Free Energy Perturbation (FEP), 11,19-22 as well as analysis through Bennett’s acceptance ratio and its variants (BAR/MBAR) 23-28 and are augmented with enhanced sampling such as replica exchange molecular dynamics, 29 metadynamics, 30 driven adiabatic free energy dynamics, 31 orthogonal space random walk, 32 adaptive integration, 33 and other methods. 34,35 Advanced alchemical free energy methods for binding affinity prediction 9,10,36 have evolved to the point that they approach quantitative predictive accuracy for ligand-binding affinities, 27,37,38 although much work remains, such as addressing sampling and convergence issues, 27,37 to improve precision so as to afford meaningful comparison with experimental uncertainties.…”