Reproducible protein folding with the stochastic tunneling method.
We report the reproducible folding of the 20 amino-acid protein trp cage using a novel version of the stochastic tunneling method and a recently developed all-atom protein free-energy force field. Six of 25 simulations reached an energy within 1 kcal/mol of the best energy, all of which correctly predicted the native experimental structure of the protein, in total eight simulations converged to the native structure. We find a strong correlation between energy and root-mean-square deviation to the native structure for all simulations.
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Forschungszentrum Karlsruhe, Institut für Nanotechnologie, 76021 Karlsruhe, Germany.
Herges
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Wenzel
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D003198:Computer Simulation; D008958:Models, Molecular; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D013269:Stochastic Processes; D013816:Thermodynamics; D014364:Tryptophan / Q000737:chemistry
D011506:Proteins; D014364:Tryptophan