Basin hopping simulations for all-atom protein folding

J Chem Phys. 2006 Jan 28;124(4):044515. doi: 10.1063/1.2138030.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation*
  • Peptides / chemistry*
  • Protein Folding*
  • Protein Structure, Secondary
  • Thermodynamics

Substances

  • Peptides
  • Trp-cage peptide