Ab initio folding of proteins with all-atom discrete molecular dynamics.

@article{Ding2008AbIF,
  title={Ab initio folding of proteins with all-atom discrete molecular dynamics.},
  author={Feng Ding and D. P. N. Tsao and Huifen Nie and Nikolay V. Dokholyan},
  journal={Structure},
  year={2008},
  volume={16 7},
  pages={1010-8}
}
Discrete molecular dynamics (DMD) is a rapid sampling method used in protein folding and aggregation studies. Until now, DMD was used to perform simulations of simplified protein models in conjunction with structure-based force fields. Here, we develop an all-atom protein model and a transferable force field featuring packing, solvation, and environment-dependent hydrogen bond interactions. We performed folding simulations of six small proteins (20-60 residues) with distinct native structures… CONTINUE READING

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