PMF score

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 ]. 

Figure 8 Crystal structure of BANA113 bound to influenza virus neuraminidase. Docked conformations ranking first (correct) and eleventh (incorrect) in a DOCK/PMF score docking experiment are compared to the crystallographic binding mode.

Evaluation of PMF Scoring in Docking Weak Ligands to the FK506 Binding Protein. 

Figure 6.19. PMF score calculated for 132 protein-ligand complexes taken from the PDB without overlap to the set of 697 complexes. The PMF score was derived from Ref 186.

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... 

Muegge I, Martin YC, Hajduk PJ, Fesik SW. Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein. J Med Chem 1999 42 2498-503. 

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]... 

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