Instantaneous normal modes as an unforced reaction coordinate for protein conformational transitions.

@article{Peng2010InstantaneousNM,
  title={Instantaneous normal modes as an unforced reaction coordinate for protein conformational transitions.},
  author={Cheng Peng and Liqing Zhang and Teresa Head-Gordon},
  journal={Biophysical journal},
  year={2010},
  volume={98 10},
  pages={
          2356-64
        }
}
We present a novel sampling approach to explore large protein conformational transitions by determining unique substates from instantaneous normal modes calculated from an elastic network model, and applied to a progression of atomistic molecular dynamics snapshots. This unbiased sampling scheme allows us to direct the path sampling between the conformational end states over simulation timescales that are greatly reduced relative to the known experimental timescales. We use adenylate kinase as… CONTINUE READING

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