Related Experiment Video
Updated: Apr 27, 2026

High-Resolution Neutron Spectroscopy to Study Picosecond-Nanosecond Dynamics of Proteins and Hydration Water
Published on: April 28, 2022
PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering
Hitesh Patel1, Björn A Grüning1, Stefan Günther1
1Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Stefan-Meier-Str. 19, D-79104 Freiburg, Germany and Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Str. 9, D-79104 Freiburg, Germany.
Summary:
Conserved water molecules play a crucial role in protein structure, stabilization of secondary structure, protein activity, flexibility and ligand binding. Clustering of water molecules in superimposed protein structures, obtained by X-ray crystallography at high resolution, is an established method to identify consensus water molecules in all known protein structures of the same family. PyWATER is an easy-to-use PyMOL plug-in and identifies conserved water molecules in the protein structure of interest. PyWATER can be installed via the user interface of PyMOL. No programming or command-line knowledge is required for its use.
Availability And Implementation:
PyWATER and a tutorial are available at https://github.com/hiteshpatel379/PyWATER. PyMOL is available at http://www.pymol.org/ or http://sourceforge.net/projects/pymol/.
Contact:
stefan.guenther@pharmazie.uni-freiburg.de.
Related Concept Videos
Aquaporins
Protein Folding
Protein Folding
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Conserved Binding Sites

