Crystal empirical scoring functions

In most empirical scoring functions, a hydrophobic character is attributed to several atom types, with equivalent weight for all hydrophobic contributions. In a more sophisticated approach, the propensity of particular atom types to be solvent-exposed or embedded in the interior of a protein can be assessed by so-called atomic solvation parameters. These have been derived, for example, from experimental octanol/water partition coefficients (303, 304) or from protein crystal structures (305, 306). Atomic solvation parameters are used in the VALIDATE scoring function (307) and have been tested in DOCK (308). 

Generally, several hundred unique crystal packings remain after optimization. They must then be evaluated with respect to either calculated physical properties such as density and lattice energy, or by means of empirical scoring functions ". ... 

Martin, E.J. and Sidlivan, D.C. (2008) AutoShim empirically corrected scoring functions for quantitative docking with a crystal structure and IC50 training data. Journal of Chemical Information and Modeling, 48, 861-872. 

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