vanddraabe: Identification and Statistical Analysis of Conserved Waters Near Proteins

vanddraabe provides a powerful way to identify and analyze conserved waters within crystallographic protein structures and molecular dynamics simulation trajectories. Statistical parameters for each water cluster, informative graphs, and a PyMOL session file to visually explore the conserved waters and protein are returned. Hydrophilicity is the propensity of waters to congregate near specific protein atoms and is related to conserved waters. An informatics derived set of hydrophilicity values are provided based on a large, high-quality X-ray protein structure dataset.

This package is a reimplementation and expansion of the WatCH¹ and PyWATER² applications and was created to provide the following abilities:

• Perform conserved water analysis on RCSB files and molecular dynamics simulations
• Provide access to data at each step of the analysis
• Provide detailed statistical summaries for all waters being analyzed
• Ability to analyze more than 65,000 waters
• Create preformatted analysis plots
• Create PyMOL session scripts to visualize the conserved waters
• Write out an Excel workbook of initial, intermediate, and final results
• Perform protein alignment using bio3d (CRAN, website, and BitBucket), an opensource applicaiton

1. Paul C Sanschagrin and Leslie A Kuhn. Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity. Protein Science, 1998, 7 (10), pp 2054-2064.
   DOI: 10.1002/pro.5560071002
   PMID: 9792092
   WatCH webpage

2. Hitesh Patel, Bjorn A. Gruning, Stefan Gunther, and Irmgard Merfort. PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering. Bioinformatics, 2014, 30 (20), pp 2978-2980.
   DOI: 10.1093/bioinformatics/btu424
   PMID: 24990608
   PyWATER on GitHub

Installing vanddraabe

vanddraabe is available on GitHub and on CRAN. To install it:

# The easiest way to get vanddraabe is:
install.packages("vanddraabe")

# Or get the development version from GitHub:
# install.packages("devtools")
devtools::install_github("exeResearch/vanddraabe")

How to use vanddraabe

The vignette provided here is a detailed example of using vanddraabe to identify the conserved waters of ten Thrombin structures.

Have a suggestion? Need help? Found a bug?

• Contact Emilio at emilio@exeResearch.com
• Submit an issue via GitHub

Code of conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.