Comparison of Stochastic optimization methods for all-atom folding of the Trp-cage protein

Abstract

The performances of three different stochastic optimization methods for all-atom protein structure prediction are investigated and compared. We use the recently developed all-atom free-energy force field (PFF01), which was demonstrated to correctly predict the native conformation of several proteins as the global optimum of the free energy surface. The trp-cage protein (PDB-code 1L2Y)is foldedwith stochastic tunneling method, a modified parallel termpering method, and the basin-hopping technique. All the methods correctly identify the native conformation, and their relative efficency is discussed.