KNOWLEDGE-BASED POTENTIALS - BACK TO THE ROOTS

Applications of knowledge-based quantities in protein structure theory are well established but their theoretical foundation, physical inter pretation, and range of applicability seems unclear or even controvers ial. Moreover, the current literature contains terms like ''pseudo-ene rgy'', ''energy-like quantity'', or ''true energy'' which are vague an d unclear and terms like ''mean-force potential'' corresponding to wel l defined concepts. Seemingly contradictory results are often caused b y inconsistent terminology. Often such problems are resolved when the physical nature of the involved quantities is properly defined. We sum marize the fundamental principles of mean-force potentials and radial distribution functions as defined in statistical mechanics and put the se into perspective with the term ''knowledge-based potential''.