Outline of the knowledgebased scoring function

The idea of deriving knowledge-based potentials for scoring protein-ligand complexes has been inspired by the success of similar potentials in folding and protein structure evaluation [34-36]. Protein-ligand atom pair potentials can be calculated from structural data alone under the assumption that an observed crystallographic complex represents the optimum placement of the ligand atoms relative to the protein atoms constrained by covalent bonds.

Considering hundreds of complexes in the PDB, there are millions of observed distances between ligand and protein atoms. Statistical potentials can be derived between protein and ligand atom types that are similar but not strictly equal to potentials of mean force [33,37]. Nevertheless, due to the familiarity with the term, we call them here potentials of mean force (PMF).

The PMF score is calculated as sum over all protein-ligand atom pair interaction free energies AtJ (r) as function of the atom pair distance r by

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