VPLG Compute and visualize protein graphs
Download

VPLG Ranking & Summary

VPLG Tags

graph protein graph viewer protein graph graph visualizer

VPLG Description

VPLG, or Visualization of Protein-Ligand Graphs is a tool that uses a graph-based model to describe the structure of proteins on the super-secondary structure level. A protein-ligand graph is computed from the atomic coordinates in a PDB file and the secondary structure assignments of the DSSP algorithm. In this graph, vertices represent secondary structure elements (SSEs, e.g. usually alpha helices and beta sheets) or ligand molecules while the edges model contacts and spatial relations between them. VPLG is written in Java using the Apache Batik library for SVG output and can run on multiple platforms. Main 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 Can read and directly visualize protein graphs from .plg-files

VPLG Related Software