Enhanced sampling and applications in protein folding in explicit solvent

Details Enhanced sampling and applications in protein folding in explicit solvent Enhanced sampling and applications in protein folding in explicit solvent

2010-03-02

arxiv.org/abs/1003.0464v3

Physics

Biological Physics

60 pages, 13 figures

Scientific paper

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 0.5~1 microsecond, all three systems were folded into atomic accuracy: the alpha carbon root mean square deviations of the best folded conformations from the native states were 0.2 A, 0.4 A, and 0.4 A, for trpzip2, trp-cage, and villin headpiece, respectively.

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