## Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015

- Nan-Jie Deng, William F. Flynn, +6 authors Ronald M. Levy
- Journal of Computer-Aided Molecular Design
- 2016

@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} }

- Published 2016 in Journal of chemical theory and computation
DOI:10.1021/acs.jctc.6b00134

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