title: 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 folded with the stochastic tunneling method, a modified parallel tempering method, and the basin-hopping technique. All the methods correctly identify the native conformation, and their relative efficiency is discussed.
authors.affiliation: Forschungszentrum Karlsruhe, Institut für Nanotechnologie, P.O. Box 3640, 76021 Karlsruhe, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Schug
authors.forename: Thomas
authors.initials: T
authors.lastname: Herges
authors.forename: Abhinav
authors.initials: A
authors.lastname: Verma
authors.forename: Kyu Hwan
authors.initials: KH
authors.lastname: Lee
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Wenzel
mesh_terms: D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
chemical_list: D010455:Peptides; C508725:Trp-cage peptide