Protein Data Bank scoring functions

Besides differences in the functional form and reference state, from a more practical point of view, the knowledge-based potentials differ also with respect to scope of atom type definitions and the amount of structural data used for their derivation. The number of different atom types ranges from 17 in Drug-Score to 40 nonmetal atom types in BLEEP. In all cases, the Protein Data Bank (321) was the source of the solved crystal structures. For BEEEP 351 selected complexes were used, whereas the PMF function was extracted from 697 complexes, and DrugScore was derived using 1376 complexes. In the latter case, the data have been extracted from Relibase (322,323). 

Complexes used to generate the empirical scoring function. The protein data bank codes [1] of the complex are given. 

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