Basin hopping simulations for all-atom protein folding
- Authors
- Verma, A; Schug, A; Lee, KH; Wenzel, W
- Issue Date
- 2006-01-28
- Publisher
- AMER INST PHYSICS
- Citation
- JOURNAL OF CHEMICAL PHYSICS, v.124, no.4
- Abstract
- 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.
- Keywords
- STOCHASTIC OPTIMIZATION METHODS; PARALLEL TEMPERING METHOD; TRP-CAGE PROTEIN; STRUCTURE PREDICTION; ENERGY LANDSCAPES; GLOBAL OPTIMIZATION; VILLIN HEADPIECE; FORCE-FIELD; MODEL; MINIMIZATION; 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
- ISSN
- 0021-9606
- URI
- https://pubs.kist.re.kr/handle/201004/135806
- DOI
- 10.1063/1.2138030
- Appears in Collections:
- KIST Article > 2006
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