In lead optimization, experiments may require difficult synthesis and thus be costly and slow. Therefore, during optimization, more accurate, but also more computationally expensive methods, such as free energy calculations, are used to prioritize the synthesis of compounds based on the in silico predictions. Although all these methods are routinely applied in drug discovery projects, improvements in their accuracy are still needed to increase their impact. The binding free energy, ∆G • , is defined as the difference between the free energy of the ligand in solution at a standard reference concentration, and the free energy of the ligand bound to the protein. This property can be calculated in a variety of ways, but two -which we consider here -are becoming relatively more common. In the so-called "absolute" approach, the ∆G • is calculated for each ligand independently. Alternatively, the "relative" approach determines the difference in binding free energy, ∆∆G • , between the binding of two ligands. In the latter case, commonly only atoms which differ between the two molecules are transformed, and the absolute binding free energy can be obtained if the binding free energy of one of the ligands is known. This relative approach, then, is most suitable for comparing or ranking binding of related ligands.