Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction

摘要

In this paper, we introduce a method to account for the shape of the potential energy curve in the evaluation of conformational free energies. The method is based on a procedure that generates a set of conformations, each with its own force-field energy, but adds a term to this energy that favors conformations that are close in structure (have a low rmsd) to other conformations. The sum of the force-field energy and rmsd-dependent term is defined here as the "colony energy" of a given conformation, because each confor- mation that is generated is viewed as representing a colony of points. The use of the colony energy tends to select conformations that are located in broad energy basins.