The importance of water molecules in the design of new compounds through structure-based drug discovery has been repeatedly established. Methods like WaterMap, WatCH, and PyWATER underscore the need for accessible methods to identify and understand the nature of binding site and structural water molecules. The inclusion of conserved waters for structure-based design studies facilitates realistic docking, the ability to consider replacing waters with polar functional groups to satisfy hydrogen bonding networks, and conservation of hydrogen bonding networks and electron transport through waters. Including highly and moderately – and possibly minor – conserved waters in a protein structure prior to solvation for molecular dynamics simulations insures all regions of the protein are solvated; especially buried regions of the protein experimentally determined to be solvated.<br/><br/>Recently the PyWATER plug-in for PyMOL reintroduced the WatCH methodology to scientists more familiar with GUIs than the command line. While PyWATER is a great plug-in and provides similar result as WatCH – conserved water clusters – it favors informative graphical information for statistical information about the water clusters. The vanddraabe package returns statistical parameters for each cluster, informative graphs, and a PyMOL session file to visually explore the conserved waters and protein. Several conserved water examples are demonstrated.<br/>

Vanddraabe: Identification and statistical analysis of structurally conserved waters via R

253rd National Meeting (2017)

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