Coarse master equations for peptide folding dynamics.

@article{Buchete2008CoarseME,
  title={Coarse master equations for peptide folding dynamics.},
  author={Nicolae-Viorel Buchete and Gerhard Hummer},
  journal={The journal of physical chemistry. B},
  year={2008},
  volume={112 19},
  pages={
          6057-69
        }
}
We construct coarse master equations for peptide folding dynamics from atomistic molecular dynamics simulations. A maximum-likelihood propagator-based method allows us to extract accurate rates for the transitions between the different conformational states of the small helix-forming peptide Ala5. Assigning the conformational states by using transition paths instead of instantaneous molecular coordinates suppresses the effects of fast non-Markovian dynamics. The resulting master equations are… CONTINUE READING

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