An Inverse Equilibrium Maximum Entropy Algorithm Applied to Proteins

Abstract

A computational method is developed to work on an inverse equilibrium problem with an interest towards applications with protein folding. In general, we are given a set of equilibrium confgiurations and want to derive the most probable potential function that results in these configurations. The method is applied to polymer simulations and a simple model of proteins using protein structures obtained from the Protein Data Bank http://www.rcsb.org/pdb The resulting energy function is tested on a few decoy sets with limited success.