Identification and Statistical Analysis of Conserved Waters in Proteins

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.


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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:

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?

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.

News

vanddraabe 1.0.0

  • Identify and provide statistical analysis of clustered waters from a collection of 3D protein structure
    • deposited in the RCSB
    • from an in-house crystallography study
    • a molecular dynamics simulation
  • Initial version

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("vanddraabe")

1.0.0 by Emilio Xavier Esposito, 10 months ago


http://www.exeResearch.com/vanddraabe.html, https://github.com/exeResearch/vanddraabe/


Report a bug at https://github.com/exeResearch/vanddraabe/issues


Browse source code at https://github.com/cran/vanddraabe


Authors: Emilio Xavier Esposito [aut, cre]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports bio3d, cowplot, fastcluster, ggplot2, openxlsx, reshape2, scales

Suggests knitr, rmarkdown, testthat


See at CRAN