WATsite

Overview

WATsite allows for the prediction of hydration site location and thermodynamic profiling using MD simulations of a protein in explicit water.

For more details please see:

  1. Masters MR, Mahmoud AH, Yang Y, Lill MA. Efficient and Accurate Hydration Site Profiling for Enclosed Binding Sites. J Chem Inf Model. 2018 Nov 26;58(11):2183-2188. doi: 10.1021/acs.jcim.8b00544.
  2. Yang Y, Abdallah AHA, Lill MA. Calculation of Thermodynamic Properties of Bound Water Molecules. Methods Mol Biol. 2018;1762:389-402. doi: 10.1007/978-1-4939-7756-7_19.
  3. Yang Y, Hu B, Lill MA. WATsite2.0 with PyMOL Plugin: Hydration Site Prediction and Visualization. Methods Mol Biol. 2017;1611:123-134. doi: 10.1007/978-1-4939-7015-5_10.
  4. Yang Y, Lill MA. Dissecting the Influence of Protein Flexibility on the Location and Thermodynamic Profile of Explicit Water Molecules in Protein-Ligand Binding. J Chem Theory Comput. 2016 Sep 13;12(9):4578-92. doi: 10.1021/acs.jctc.6b00411. Epub 2016 Aug 18.
  5. Hu B, Lill MA. WATsite: hydration site prediction program with PyMOL interface. J Comput Chem. 2014 Jun 15;35(16):1255-60. doi: 10.1002/jcc.23616.
  6. Hu B, Lill MA. Protein pharmacophore selection using hydration-site analysis. J Chem Inf Model. 2012 Apr 23;52(4):1046-60. doi: 10.1021/ci200620h.

Please, feel free to use and modify our plugins. Please, contact us (mlill@purdue.edu, abdallah@purdue.edu) if you find bugs and have recommendation for improved versions of our software.