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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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Related Experiment Video

Updated: Mar 3, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
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WATsite2.0 with PyMOL Plugin: Hydration Site Prediction and Visualization.

Ying Yang1, Bingjie Hu1,2, Markus A Lill3

  • 1Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN, 47907, USA.

Methods in Molecular Biology (Clifton, N.J.)
|April 29, 2017
PubMed
Summary

WATsite identifies crucial water molecules in protein binding sites using molecular dynamics simulations. This helps understand protein function and estimate ligand binding free energy.

Keywords:
Hydration sitesMolecular dynamicsProtein desolvation free energy

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Area of Science:

  • Structural biology
  • Computational chemistry
  • Biophysics

Background:

  • Water molecules in protein binding sites are critical for protein structure, function, and ligand interactions.
  • Understanding the location and thermodynamic contributions of these water molecules is essential for deciphering protein mechanisms.
  • Water displacement is a key driving force in ligand binding, highlighting the importance of hydration analysis.

Purpose of the Study:

  • To introduce WATsite, a novel program with a graphical user interface (GUI) for analyzing hydration sites in proteins.
  • To identify and characterize explicit water molecules within protein binding sites using molecular dynamics (MD) simulation trajectories.
  • To enable the estimation of protein desolvation free energy for ligands by analyzing displaced hydration sites.

Main Methods:

  • Utilizing molecular dynamics (MD) simulation trajectories to identify hydration sites.
  • Employing the WATsite program, integrated with a PyMOL-based GUI, for hydration site analysis.
  • Differentiating four types of explicit water molecules and analyzing hydration sites with or without bound ligands.

Main Results:

  • WATsite successfully identifies and categorizes hydration sites within protein binding pockets.
  • The program facilitates the analysis of water molecule locations and their thermodynamic contributions to protein-ligand interactions.
  • Protein desolvation free energy can be accurately estimated by summing the free energies of displaced hydration sites.

Conclusions:

  • WATsite provides a valuable tool for researchers studying protein hydration and its role in function and ligand binding.
  • The program aids in understanding the energetic contributions of water molecules to protein-ligand binding affinity.
  • WATsite is freely available, promoting further research in structural biology and drug discovery.