Journal
JOURNAL OF CHEMICAL PHYSICS
Volume 132, Issue 24, Pages -Publisher
AMER INST PHYSICS
DOI: 10.1063/1.3435332
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Funding
- National Institutes of Health [R01-GM067801]
- National Science Foundation [MCB-0818353]
- Welch Foundation [Q-1512]
- John S. Dunn Gulf Coast Consortium for Chemical Genomics
- Rice University
- NSF [EIA-0216467]
- Div Of Molecular and Cellular Bioscience
- Direct For Biological Sciences [0818353] Funding Source: National Science Foundation
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We report a single-copy tempering method for simulating large complex systems. In a generalized ensemble, the method uses runtime estimate of the thermal average energy computed from a novel integral identity to guide a continuous temperature-space random walk. We first validated the method in a two-dimensional Ising model and a Lennard-Jones liquid system. It was then applied to folding of three small proteins, trpzip2, trp-cage, and villin headpiece in explicit solvent. Within 0.5 similar to 1 microsecond, all three systems were reversibly folded into atomic accuracy: the alpha carbon root mean square deviations of the best folded conformations from the native states were 0.2, 0.4, and 0.4 angstrom, for trpzip2, trp-cage, and villin headpiece, respectively. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3435332]
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