FEP calculations have been used for studying host–guest binding energetics, pKa predictions, solvent effects on reactions, and enzymatic reactions. Other applications are the virtual screening of ligands in drug discovery, in silico mutagenesis studies and antibody affinity maturation. For the study of reactions it is often necessary to involve a quantum-mechanical (QM) representation of the reaction center because the molecular mechanics (MM) force fields used for FEP simulations cannot handle breaking bonds. A hybrid method that has the advantages of both QM and MM calculations is called QM/MM.