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RamplotR

R shiny app for making Ramachandran plots.

The calculation of the density backgrounds for the ramachadran plots is done based on the list of proteins proposed by Lovell et al. (2003).

Usage

Published version

This app is published via shinyapps.io and can be used via https://bioit.shinyapps.io/RamplotR/.

Install it yourself

  1. Install R from the website (tested using v4.03)
  2. Run the following code:
# Install the packages above if they are not already installed
installed_packages <- rownames(installed.packages())
required_packages <- c("shiny", "shinycssloaders", "shinyWidgets", "colourpicker", "bio3d", "plyr")
for (p in required_packages) {
  if (!(p %in% installed_packages)) {
    install.packages(p)
  }
}
  1. Run the app.R script

Example image of the app

Example image of the app

To be done

  • Custom PDB upload support
  • Add CIF support
  • Output a statistic output of the number of residues in each region
  • Output a list of residues in each region
  • Recalculate the density backgrounds with newer best proteins?
  • Optimize the calculation of the torsion angles (now with bio3d but can be quite slow)