Schug, A Herges, T Verma, A Lee, KH Wenzel, W 2024-01-21T04:01:33Z 2024-01-21T04:01:33Z 2021-09-02 2005-12-09 1439-4235 https://pubs.kist.re.kr/handle/201004/135892 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. English WILEY-V C H VERLAG GMBH PARALLEL TEMPERING METHOD STRUCTURE PREDICTION ENERGY LANDSCAPES GLOBAL OPTIMIZATION SIMULATIONS MINIMIZATION ALGORITHMS PEPTIDES POLYPEPTIDES DYNAMICS Comparison of Stochastic optimization methods for all-atom folding of the Trp-cage protein Article 10.1002/cphc.200500213 1 CHEMPHYSCHEM, v.6, no.12, pp.2640 - 2646 CHEMPHYSCHEM 6 12 2640 2646 scie scopus 000234002300026 2-s2.0-29144432368 Chemistry, Physical Physics, Atomic, Molecular & Chemical Chemistry Physics Article PARALLEL TEMPERING METHOD STRUCTURE PREDICTION ENERGY LANDSCAPES GLOBAL OPTIMIZATION SIMULATIONS MINIMIZATION ALGORITHMS PEPTIDES POLYPEPTIDES DYNAMICS conformation analysis optimization protein folding protein structures stochastic processes