Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials.

@article{Wang2006AbsoluteBF,
  title={Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials.},
  author={Jiyao Wang and Yuqing Deng and Beno{\^i}t Roux},
  journal={Biophysical journal},
  year={2006},
  volume={91 8},
  pages={2798-814}
}
The absolute (standard) binding free energy of eight FK506-related ligands to FKBP12 is calculated using free energy perturbation molecular dynamics (FEP/MD) simulations with explicit solvent. A number of features are implemented to improve the accuracy and enhance the convergence of the calculations. First, the absolute binding free energy is decomposed into sequential steps during which the ligand-surrounding interactions as well as various biasing potentials restraining the translation… CONTINUE READING

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