Solvent Interaction Energy Calculations on Molecular Dynamics Trajectories: Increasing the Efficiency Using Systematic Frame Selection

@article{Lill2011SolventIE,
  title={Solvent Interaction Energy Calculations on Molecular Dynamics Trajectories: Increasing the Efficiency Using Systematic Frame Selection},
  author={Markus A. Lill and Jared J. Thompson},
  journal={Journal of chemical information and modeling},
  year={2011},
  volume={51 10},
  pages={2680-9}
}
End-point methods such as linear interaction energy (LIE) analysis, molecular mechanics generalized Born solvent-accessible surface (MM/GBSA), and solvent interaction energy (SIE) analysis have become popular techniques to calculate the free energy associated with protein-ligand binding. Such methods typically use molecular dynamics (MD) simulations to generate an ensemble of protein structures that encompasses the bound and unbound states. The energy evaluation method (LIE, MM/GBSA, or SIE) is… CONTINUE READING