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Bioinformatics. 2014 Oct 15;30(20):2978-80. doi: 10.1093/bioinformatics/btu424. Epub 2014 Jul 1.

PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering.

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  • 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.



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.


PyWATER and a tutorial are available at PyMOL is available at or


© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail:

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