Finite Temperature String Method with Umbrella Sampling: Application on a Side Chain Flipping in Mhp1 Transporter.

@article{Song2017FiniteTS,
  title={Finite Temperature String Method with Umbrella Sampling: Application on a Side Chain Flipping in Mhp1 Transporter.},
  author={Hyun Deok Song and Fangqiang Zhu},
  journal={The journal of physical chemistry. B},
  year={2017},
  volume={121 15},
  pages={3376-3386}
}
Protein conformational change is of central importance in molecular biology. Here we demonstrate a computational approach to characterize the transition between two metastable conformations in all-atom simulations. Our approach is based on the finite temperature string method, and the implementation is essentially a generalization of umbrella sampling simulations with Hamiltonian replica exchange. We represent the transition pathway by a curve in the conformational space, with the curve… CONTINUE READING
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