Statistical energy potential: reduced representation of Dehouck–Gilis–Rooman function by selecting against decoy datasets

Abstract

Statistical effective energy function (SEEF) is derived from the statistical analysis of the database of known protein structures. Dehouck-Gilis-Rooman (DGR) group has recently created a new generation of SEEF in which the additivity of the energy terms was manifested by decomposing the total folding free energy into a sum of lower order terms. We have tried to optimize the potential function based on their work. By using decoy datasets as screening filter, and through modification of algorithms in calculation of accessible surface area and residue-residue interaction cutoff, four new combinations of the energy terms were found to be comparable to DGR potential in performance test. Most importantly, the term number was reduced from the original 30 terms to only 5 in our results, thereby substantially decreasing the computation time while the performance was not sacrificed. Our results further proved the additivity and manipulability of the DGR original energy function, and our new combination of the energy could be used in prediction of protein structures.