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vplg (9)
Tim Schäfer

VPLG

Welcome to the Visualization of Protein Ligand Graphs (VPLG) Sourceforge website!

VPLG 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, usually alpha helices and beta strands) or ligand molecules while the edges model contacts and relative orientations between them.

Example output

VPLG is written in Java using the Apache Batik library for SVG output. Database connectivity (optional) is provided by the PostgreSQL JDBC driver. VPLG was tested on Linux and Windows and should also run under MacOS.

This website is used to provide the online VPLG [Documentation]. Some of this information is also available in the doc/ directory of your release. VPLG is a software package consisting of the following tools:

  • [PLCC] -- The Protein Ligand Contact Calculation (PLCC) tool is the core component. It is a command line application written in Java that computes and visualizes protein-ligand graphs.
  • [VPG] -- This is a simple and optional graphical user interface (GUI) for PLCC. It allows you to set the file system paths to the other programs and select a PDB file to process. It will then generate the proper command line and execute PLCC for you.
  • [SplitPDB] -- This tool can be used to extract data on a specific model (the 1st one by default) from a PDB file. This is required if the PDB file contains multiple models because the DSSP program does not support files with multiple models.

If this is the 1st time you read about VPLG, you may want to know more details on [How_it_works]. In that case, you may also want some help on how to interpret the graph images. I suggest you read [PLCC_Graphtypes] to get started.

Input data:
The VPLG software package uses 3D atom data from PDB files and secondary structure element (SSE) assignments from DSSP files (Kabsch & Sander 1983). You can download DSSP files for many PDB entries from the DSSP database via RMS or generate them for your private PDB files at this server. You can also download the DSSP program from the DSSP website and generate them yourself though. The VPG GUI of our software now comes with a downloader that allows you to download both the PDB and DSSP file for some PDB protein with a single click!

If you need the Source code of VPLG, go here: [Code]. You may also be interested in the [License] of VPLG or in information on how to cite VPLG or contact the author (see [Citing]).

A webserver to download pre-computed graphs in various formats is in the works, for now use this page: [Download_Graphs].


Related

Wiki: Citing
Wiki: Code
Wiki: Documentation
Wiki: Download_Graphs
Wiki: How_it_works
Wiki: License
Wiki: PLCC
Wiki: PLCC_Graphtypes
Wiki: SplitPDB
Wiki: VPG