PMF scoring function

Muegge and Martin introduced a ligand volume correction to the reference state when deriving their PMF scoring function [47]. The mean-force potential between a protein atom of type i and a ligand atom of type j was expressed as... 

Knowledge-based functions are based on the derivation of statistical preferences in the form of potentials for protein ligand atom pair interactions. Similar to potentials derived for protein folding and protein structure evaluation (e.g., Ref. 148), pair potentials akin to potentials of mean force (PMFs) are derived for various protein and ligand atom types using the PDB as a knowledge base. The PMF scoring function [118]... 

The calculation of the binding affinity with con.sidcration of all tbc.se effects for virtual screening is not possible. In order to circumvent thus difficulty, scoring functions arc used instead, c.g., the Liidi scoring function [80, or consensus scoring functions derived from FlevX score, DOCK score, GOLD score, ChemScore, or PMF score [81 ]. 

Chemscore Cscore Regression-based scoring function Suite of scoring functions (ChemScore, DOCK, FlexX, GOLD, PMF) and consensus scoring tool... 

Table 1 Correlations of binding affinity prediction for seven published knowledge-based scoring functions for the PMF validation sets of 77 protein-ligand complexes (all) which consist of five classes [47] 16 serine protease (Ser), 15 metalloprotease (Met), 18 L-arabinose binding protein (L-ara), 11 endothiapepsin (End), and 17 diverse protein-ligand complexes (Oth)... 

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