Complementarity score

The earliest designers of scoring functions recognized two fundamental contributions to receptor-ligand complementarity shape and electrostatics. To account for 3D shape complementarity, they calculated some form of contact or van der Waals score, and to account for electrostatic interactions, they calculated some form of electrostatic potential score. In 1992 Kuntz and coworkers... 

Figure 12 Conformation of statherin on HAp surface determined by molecular modelling. The four basic residues (K6, R9, RIO, and R13) fit nicely to the IPOT motif (outlined in dots). FADE scores are quantitative measure of shape complementarity. (Reprinted with permission from Ref. 181. 2007 American Chemical Society.)...

Unreasonable docked binding mode. Fast docking tools cannot produce reliable solutions for all compounds often, even some well-scoring compounds are simply docked to the outer surface of the protein or adopt rather strained conformations to achieve good surface complementarity within the binding pocket. Computational filters help to detect such situations (329). 

The PEP function, for example, addresses general steric complementarity and hydro-phobic interactions based on rather long-range pair potentials, whereas the FlexX score concentrates on hydrogen-bond complemen-... 

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