Structure-derived potentials and protein simulations.

Abstract

There has recently been an explosion in the number of structure-derived potential functions that are based on the increasing number of high-resolution protein crystal structures. These functions differ principally in their reference states; the usual two classes correspond either to initial solvent exposure or to residue exposure of residues. Reference states are critically important for applications of these potentials functions. Inspection of the potential functions and their derivation can tell us not only about protein interaction strengths themselves, but can also provide suggestions for the design of better folding simulations. An appropriate goal in this field is achieving self-consistency between the details in the derivation of potentials and the applied simulations.