Analysis of Factors Influencing Hydration Site Prediction Based on Molecular Dynamics Simulations

@inproceedings{Yang2014AnalysisOF,
  title={Analysis
of Factors Influencing Hydration Site Prediction
Based on Molecular Dynamics Simulations},
  author={Ying Yang and Bingjie Hu and Markus A. Lill},
  booktitle={Journal of Chemical Information and Modeling},
  year={2014}
}
Water contributes significantly to the binding of small molecules to proteins in biochemical systems. Molecular dynamics (MD) simulation based programs such as WaterMap and WATsite have been used to probe the locations and thermodynamic properties of hydration sites at the surface or in the binding site of proteins generating important information for structure-based drug design. However, questions associated with the influence of the simulation protocol on hydration site analysis remain. In… CONTINUE READING