Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation.

@article{Mentes2016BindingED,
  title={Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation.},
  author={Ahmet Mentes and Nan-Jie Deng and R. S. K. Vijayan and Junchao Xia and Emilio Gallicchio and Ronald M. Levy},
  journal={Journal of chemical theory and computation},
  year={2016},
  volume={12 5},
  pages={2459-70}
}
Molecular dynamics modeling of complex biological systems is limited by finite simulation time. The simulations are often trapped close to local energy minima separated by high energy barriers. Here, we introduce Hamiltonian replica exchange (H-REMD) with torsional flattening in the Binding Energy Distribution Analysis Method (BEDAM), to reduce energy barriers along torsional degrees of freedom and accelerate sampling of intramolecular degrees of freedom relevant to protein-ligand binding. The… CONTINUE READING