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Visualization of Protein-Ligand Graphs

Posted on by Robin Ding Leave a comment Bio-Informatics, Molecular Science, Visualization

The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm.

VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/

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Website http://rcmd.org/vplg/
Tags
License GNU General Public License version 2.0 (GPLv2)
Platform BSD Linux Mac Windows
Features
  • Reads 3-dimensional atom data from PDB files and secondary structure assignments from DSSP files
  • Computes a protein-ligand graph from the data and visualizes the graph
  • Supports output of the graph images in bitmap (.png) and vector (.svg) formats
  • Exports protein-ligand graphs in a plain text file in its own format (.plg) that is easy to edit, parse and generate with a computer program as well as in a number of standard graph file formats
  • Can read and directly visualize protein graphs from .plg-files
  • Free Open Source Software (FOSS)
  • Database support (completely optional, no database server required by default)
  • Command line interface allows for easy batch processing via shell scripts
  • Allows filtering of ligands by atom number
  • New GUI written in Java, no need to type console commands anymore!
  • The software that powers the PTGL web server: http://ptgl.uni-frankfurt.de/