Verma, A Schug, A Lee, KH Wenzel, W 2024-01-21T03:40:35Z 2024-01-21T03:40:35Z 2021-09-01 2006-01-28 0021-9606 https://pubs.kist.re.kr/handle/201004/135806 We investigate different protocols of the basin hopping technique for de novo protein folding. Using the protein free-energy force field PFF01 we report the reproducible all-atom folding of the 20-amino-acid tryptophan-cage protein [Protein Data Bank (PDB) code: 112y] and of the recently discovered 26-amino-acid potassium channel blocker (PDB code: 1wqc), which exhibits an unusual fold. We find that simulations with increasing cycle length and random starting temperatures perform best in comparison with other parametrizations. The basin hopping technique emerges as a simple but very efficient and robust workhorse for all-atom protein folding. (c) 2006 American Institute of Physics. English AMER INST PHYSICS STOCHASTIC OPTIMIZATION METHODS PARALLEL TEMPERING METHOD TRP-CAGE PROTEIN STRUCTURE PREDICTION ENERGY LANDSCAPES GLOBAL OPTIMIZATION VILLIN HEADPIECE FORCE-FIELD MODEL MINIMIZATION Basin hopping simulations for all-atom protein folding Article 10.1063/1.2138030 1 JOURNAL OF CHEMICAL PHYSICS, v.124, no.4 JOURNAL OF CHEMICAL PHYSICS 124 4 scie scopus 000234979300052 2-s2.0-33749665952 Chemistry, Physical Physics, Atomic, Molecular & Chemical Chemistry Physics Article STOCHASTIC OPTIMIZATION METHODS PARALLEL TEMPERING METHOD TRP-CAGE PROTEIN STRUCTURE PREDICTION ENERGY LANDSCAPES GLOBAL OPTIMIZATION VILLIN HEADPIECE FORCE-FIELD MODEL MINIMIZATION de nono protein folding basin hopping force filed PFF01 20 amino acid trp cage