Ligand surface interaction energy

Both the protein and the ligand are solvated by water when they are separated. As the two surfaces interact, water is excluded, hydrogen bonds are broken and formed, hydrophobic interactions occur, and the protein and ligand stick to each other. As in protein folding and for the same reasons, the hydrophobic interaction provides much of the free energy for the association reaction, but polar groups that are removed... 

Force-field-based scoring functions use arbitrary empirical estimates of interaction energies obtained by molecular mechanics energy functions. This simple approximation, which takes into account only enthalpic contribution often correlates well with the experiment. Solvent effects are described by atom-based solvation parameters, which are computed for the surface of both ligand and receptor which is buried upon complexation. DOCK-chemical27 and CHARMm scoring functions represent this class. 

Molecular descriptors based on hydrophobic interaction energy between nonpolar surfaces of ligand and receptor. The energy of hydrophobic interactions derives from the disruption of the water structme around nonpolar surfaces resulting in a gain of entropy [Abraham and Kellogg, 1993]. 

---