Comparison of stochastic optimization methods for all-atom folding of the Trp-Cage protein.
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.
Schug
Alexander
A
Forschungszentrum Karlsruhe, Institut für Nanotechnologie, P.O. Box 3640, 76021 Karlsruhe, Germany.
Herges
Thomas
T
Verma
Abhinav
A
Lee
Kyu Hwan
KH
Wenzel
Wolfgang
W
D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
D010455:Peptides; C508725:Trp-cage peptide