Efficient Sampling of Protein Structures by Model Hopping
- 22 September 2005
- journal article
- research article
- Published by American Physical Society (APS) in Physical Review Letters
- Vol. 95 (13) , 138102
- https://doi.org/10.1103/physrevlett.95.138102
Abstract
We introduce a novel simulation method, model hopping, that enhances sampling of low-energy configurations in complex systems. The approach is illustrated for a protein-folding problem. Thermodynamic quantities of proteins with up to 46 residues are evaluated from all-atom simulations with this method.Keywords
This publication has 20 references indexed in Scilit:
- 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
- On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure predictionThe Journal of Chemical Physics, 2002
- Generalized parallel samplingPhysica A: Statistical Mechanics and its Applications, 2002
- Global Optimization by Energy Landscape PavingPhysical Review Letters, 2002
- Multi-Self-Overlap Ensemble for Protein Folding: Ground State Search and ThermodynamicsPhysical Review Letters, 1999
- 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