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Bioinformatics. 2014 Jul 1. pii: btu424. [Epub ahead of print]

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

Author information

  • Pharmaceutical 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.

Abstract

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.

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

PMID:
24990608
[PubMed - as supplied by publisher]
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