Journal
JOURNAL OF CHEMICAL PHYSICS
Volume 121, Issue 1, Pages 415-425Publisher
AMER INST PHYSICS
DOI: 10.1063/1.1738647
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We propose an efficient method for the prediction of protein folding rate constants and mechanisms. We use molecular dynamics simulation data to build Markovian state models (MSMs), discrete representations of the pathways sampled. Using these MSMs, we can quickly calculate the folding probability (P-fold) and mean first passage time of all the sampled points. In addition, we provide techniques for evaluating these values under perturbed conditions without expensive recomputations. To demonstrate this method on a challenging system, we apply these techniques to a two-dimensional model energy landscape and the folding of a tryptophan zipper beta hairpin. (C) 2004 American Institute of Physics.
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