Figure 1. The Lennard–Jones potential models the van der Waals interaction and steric repulsion between a pair of atoms. The precise shape of the curve is dependent upon the atom types. In each case, however, the characteristic shape has a favourable ‘well’ near the position of the global minimum, a steep barrier to atomic collision, and a ‘tail’ that quickly tends toward zero.

Figure 2. The thermodynamic cycle is a convenient way to calculate the desolvation penalty for binding two proteins in solution. The change in free energy for binding in solution is equal to the change in free energy for binding in vacuum plus the difference between the free energy for solvating the molecules as a complex and individually.

Figure 3. A ‘united atom’ model combines heavy atoms, such as carbon and nitrogens, with their bound hydrogens in order to create meta-atoms that reflect the size and biochemical properties of the group. In the figure, a benzene molecule has been recast as two CH₃ groups and two CH₂ groups. This provides computational efficiency when doing energy calculations, since the 14-atom benzene molecule has been replaced with four united atoms. Polar hydrogens should not be modelled using united atoms, since atomic level detail of hydrogen bonds is desirable.