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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.

How it works

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.

Example output

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. This tool is outdated, and does not come with the latest versions of VPLG anymore.
  • [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]).

New to the command line?

Note that PLCC and SplitPDB are command line programs, i.e., you have to run them from a shell prompt. If you have never done this before, don't worry. We have a step-by-step guide that will get you up and running: [PLCC_from_shell]

Prefer a web server?

If you just do not like the command line, you can access pre-computed VPLG output on our webserver. The PTGL serves the VPLG results for the whole RCSB PDB, and is available at http://ptgl.uni-frankfurt.de/.

For developers: Code moved to GitHub

Starting on July 29, 2015, the development of VPLG is now happening at GitHub: https://github.com/dfsp-spirit/vplg

We will continue to use this website at Sourceforge for releases and other stuff. So if you are not a developer, nothing changes for you. If you are a developer, you will notice that the repo here at SF is now read-only, and that you cannot commit to it anymore. Please contact Tim Schaefer to get access to the repo at GitHub in that case. Please tell me your GitHub username in the email. Also note that the code in the repo here at SF no longer gets updated, so do NOT use it or send any patches against it. Use the latest code at GitHub instead!


Related

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