Algorithm and Data Structures for Efficient Energy Maintenance during Monte Carlo Simulation of Proteins

@article{Lotan2004AlgorithmAD,
  title={Algorithm and Data Structures for Efficient Energy Maintenance during Monte Carlo Simulation of Proteins},
  author={Itay Lotan and F. Schwarzer and D. Halperin and J. Latombe},
  journal={Journal of computational biology : a journal of computational molecular cell biology},
  year={2004},
  volume={11 5},
  pages={
          902-32
        }
}
  • Itay Lotan, F. Schwarzer, +1 author J. Latombe
  • Published 2004
  • Mathematics, Computer Science, Medicine
  • Journal of computational biology : a journal of computational molecular cell biology
Monte Carlo simulation (MCS) is a common methodology to compute pathways and thermodynamic properties of proteins. A simulation run is a series of random steps in conformation space, each perturbing some degrees of freedom of the molecule. A step is accepted with a probability that depends on the change in value of an energy function. Typical energy functions sum many terms. The most costly ones to compute are contributed by atom pairs closer than some cutoff distance. This paper introduces a… Expand
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