Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations.

@article{Deng2008ComputationOB,
  title={Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations.},
  author={Yuqing Deng and Beno{\^i}t Roux},
  journal={The Journal of chemical physics},
  year={2008},
  volume={128 11},
  pages={115103}
}
The binding of a ligand to a receptor is often associated with the displacement of a number of bound water molecules. When the binding site is exposed to the bulk region, this process may be sampled adequately by standard unbiased molecular dynamics trajectories. However, when the binding site is deeply buried and the exchange of water molecules with the bulk region may be difficult to sample, the convergence and accuracy in free energy perturbation (FEP) calculations can be severely… CONTINUE READING

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