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

Hitesh Patel | Zendy; Björn Grüning | Zendy; Stefan Günther | Zendy; Irmgard Merfort | Zendy

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

Author(s) -

Hitesh Patel,

Björn Grüning,

Stefan Günther,

Irmgard Merfort

Publication year - 2014

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btu424

Subject(s) - molecular graphics , computer science , protein structure , protein family , software , flexibility (engineering) , plug in , protein data bank (rcsb pdb) , interface (matter) , cluster analysis , computational biology , protein data bank , sequence alignment , crystallography , programming language , chemistry , biology , data mining , computer graphics , peptide sequence , biochemistry , operating system , artificial intelligence , mathematics , statistics , bubble , maximum bubble pressure method , gene

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.

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