Knowledge-based potentials--back to the roots.

Abstract

Applications of knowledge-based quantities in protein structure theory are well established but their theoretical foundation, physical interpretation, and range of applicability seems unclear or even controversial. Moreover, the current literature contains terms like "pseudo-energy", "energy-like quantity", or "true energy" which are vague and unclear and terms like "mean-force potential" corresponding to well defined concepts. Seemingly contradictory results are often caused by inconsistent terminology. Often such problems are resolved when the physical nature of the involved quantities is properly defined. We summarize the fundamental principles of mean-force potentials and radial distribution functions as defined in statistical mechanics and put these into perspective with the term "knowledge-based potential".