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Statistical potential

From Wikipedia, the free encyclopedia

In protein structure prediction, statistical potentials or knowledge-based potentials are scoring functions derived from an analysis of known protein structures in the Protein Data Bank (PDB).

Example of interatomic pseudopotential, between β-carbons of isoleucine and valine residues, generated by using MyPMFs.[1]

The original method to obtain such potentials is the quasi-chemical approximation, due to Miyazawa and Jernigan.[2] It was later followed by the potential of mean force (statistical PMF [Note 1]), developed by Sippl.[3] Although the obtained scores are often considered as approximations of the free energy—thus referred to as pseudo-energies—this physical interpretation is incorrect.[4][5] Nonetheless, they are applied with success in many cases, because they frequently correlate with actual Gibbs free energy differences.[6]