Optimized parallel tempering simulations of proteins
- 1 May 2006
- journal article
- Published by AIP Publishing in The Journal of Chemical Physics
- Vol. 124 (17), 174903
- https://doi.org/10.1063/1.2186639
Abstract
We apply a recently developed adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an optimal set of temperatures/replicas which are found to concentrate at the bottlenecks of the simulations. A measure of convergence for the equilibration of the parallel tempering algorithm is discussed. We test our algorithm by simulating the 36-residue villin headpiece subdomain HP-36 where we find a lowest-energy configuration with a root-mean-square deviation of less than 4 Å to the experimentally determined structure.Keywords
This publication has 24 references indexed in Scilit:
- Efficient Sampling of Protein Structures by Model HoppingPhysical Review Letters, 2005
- Optimizing the ensemble for equilibration in broad-histogram Monte Carlo simulationsPhysical Review E, 2004
- Simulations of a small protein in a specifically designed generalized ensemblePhysical Review E, 2004
- Folding of the Villin Headpiece Subdomain from Random Structures. Analysis of the Charge Distribution as a Function of pHJournal of Molecular Biology, 2004
- Parallel tempering simulations of HP‐36Proteins-Structure Function and Bioinformatics, 2003
- All‐atom fast protein folding simulations: The villin headpieceProteins-Structure Function and Bioinformatics, 2002
- Native-like Mean Structure in the Unfolded Ensemble of Small ProteinsJournal of Molecular Biology, 2002
- Parallel tempering algorithm for conformational studies of biological moleculesChemical Physics Letters, 1997
- A Thermostable 35-Residue Subdomain within Villin HeadpieceJournal of Molecular Biology, 1996
- Exchange Monte Carlo Method and Application to Spin Glass SimulationsJournal of the Physics Society Japan, 1996