Reproducible protein folding with the stochastic tunneling method

Phys Rev Lett. 2003 Oct 10;91(15):158102. doi: 10.1103/PhysRevLett.91.158102. Epub 2003 Oct 6.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation
  • Models, Molecular
  • Protein Folding*
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Reproducibility of Results
  • Stochastic Processes
  • Thermodynamics
  • Tryptophan / chemistry

Substances

  • Proteins
  • Tryptophan