Visualization of Protein-Ligand Graphs / Blog: Recent posts

Changes in this release:
-fix bug with detection of 4 helix bundle motif (false positive)
-add manual SVG format output for interactive SVG handling from JavaScript, done at the ISMB 2016 conference hackathon
-add internal options for an advanced contact model (off by default)
-save graphlet data to database and adjust schema accordingly
-many small fixes

The release is also available for download at GitHub, where development now takes place: https://github.com/dfsp-spirit/vplg/releases... read more

I have just released version 2015_09_17 of VPLG.

Changes include:
- support for ligand-centered complex graphs, which show all chains a ligand is in contact with
- fix and dramatically improve the code that draws Ramachandran plots.
- Support for marking prefered dihedral angle areas for different SSE types in Ramachandran plots.
- improve formating of font on images
- fix various small bugs

Note that I also upload release binaries to GitHub now. So you can download the release here at SourceForge, or at GitHub (where dev takes place): https://github.com/dfsp-spirit/vplg/releases

We have just added a detailed tutorial on howto run PLCC from the command line. The document is intended for users who are new to the shell/terminal/command prompt.

If you have never run a program from the command line and want to run PLCC, start here: https://sourceforge.net/p/vplg/wiki/PLCC_from_shell/

Note that a user-friendly web server is also available. The Protein Topology Graph Library (PTGL) server gives you access to PLCC output for the whole RCSB PDB. Check it out at http://ptgl.uni-frankfurt.de/

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 though. So if you are not a developer, nothing changes for you at this time.

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.... read more

The VPLG software can now be found on twitter, checkout https://twitter.com/vplg_project and follow @vplg_project if you are interested!

We just released a new VPLG version. Apart from large internal changes, this release adds new features and fixes some known bugs.

Most important fixes:
* fixes a bug in the ADJ and RED notation strings, which would omit distances for z-edges if the target vertex they jump to has a degree of 2 or more

Most important new features:
* draw graphs in GML format from the command line
* new graph output format: GEFX

We just released a new version of VPLG.

This is a bugfix release, which contains many small fixes. The most important one is that the visualization of folding graphs in KEY notation was broken in the old release. This is fixed now, along with various other small bugs.

A new version of VPLG has been released. This is a large feature and bugfix release. The list of changes and features is endless, here are some examples from the release log:

• ALL: changed license to GPL 2.0
• PLCC
• support for computing folding graphs (connected components of protein graphs)
• support for computing linear notation strings for all 4 FG notations
• support for drawing all 4 FG notations
• database schema changed (a lot!), index optimization, denormalization for performance reasons for very large DBs (whole PDB)
• proper silent mode
• cluster mode, which keeps the chains file for GraphletAnalyzer and other stuff
• new output formats: GXMML (XML), JSON, and others
• ...
• VPG
• the VPG GUI is very outdated and has been removed. We will redesign it from scratch and add a new version once its ready.... read more

Starting with revision 1157, the license of VPLG has been changed to the GNU public license 2.0.

The reason is that this license is more common, and that I want a viral open source license.

The next release, which will be available soon, will also use the GPL 2.0, of course.

The current SVN version of plcc (rev. 940) can now compute folding graphs (FGs). FGs are the connected components of a protein graph. Since these graphs are connected, it is possible to compute linear string notations for them (think of SMILES for small molecules). These linear notations can be used to quickly search for certain substructures in the graphs.

Protein complexes are getting more and more attention in systems biology and bioinformatics. The next release of VPLG will therefor include the option to compute complex graphs. These graphs contain the SSEs of all chains from a PDB file (instead of a single chain).

You can use complex graphs to analyze the contacts between the different sub-units of a protein complex.

These graphs can get very large, of course. Here is a first preview, the complex graph from the entire respiratory complex I from Thermus thermophilus (PDB-ID 4HEA):... read more

A new version of VPLG has been released. This is a bugfix release which improves support for parsing alternative atom location fields (AltLocs) in strange PDB files.

Examples:
PLCC can now cope with residues which have no atoms in the default location or which define several AltLocs, some of which define no alpha carbon atom.

Minor fixes to VPG are also included (see the release log for more details).... read more

A new version has been released. Folding graphs, i.e. connected components of protein ligand graphs, can now also be exported in all formats. You can also configure VPLG to add meta data (e.g., species) to exported graphs in comments (for export formats which support comments but no graph meta data).

More details are in the release log.

I recently held a talk on VPLG at the GCB 2012 conference at Jena, Germany. The slides are available here: GCB 2012 Talk on VPLG.

An article on VPLG has also been published in the conference proceedings.

Protein ligand graphs for the whole PDB are now available for download in GML format and Kavosh Edge List format.

The ZIP archives contain albelig graphs for more than 151,000 protein chains and you can download them here.

VPLG version 2012_09_14 has been released.

RELEASE LOG

Updates from version 2012-09-07 to 2012-09-14:

• PLCC:
• added option to write all PG output files (not just images) to a PDB-style subdirecotry structure (-K, -k), e.g. '<baseoutputdir>/ic/8icd/8icd_A_albelig_PG.gml')</baseoutputdir>
• fixed command line parsing of output formats, kavosh edge list format is now 'e' as described in help (it was 'k' before)

A new version of VPLG has been released. The most exciting features are two new batch processing forms for VPG. They are still experimental though, so handle with care. Full change log in the release and below:

Updates from version 2012-08-17 to 2012-09-07:
* PLCC:
- new command line option '-C' or '--create-config' to create a default config, then exit
- added Kavosh edge list output format
- changed '--outputformats' command line option, PLCC format is now a format like all others ('p') and 'x' does not write it anymore
- improvements to GML and DOT language exporters: better annotations of the graphs
- added new backbone contact type and option to force backbone contacts (-B or --force-backbone)
- comments on more DB tables
* VPG:
- updated GUI to new PLCC features
- new experimental batch frame for creating DSSP files from PDB input files (using SplitPDB and dsspcmbi)
- new experimental batch frame for creating graphs from PDB and DSSP files
- many small bug fixes

A new release with some bug fixes for PLCC and VPG has been published. It adds the fixes from SVN, most importantly proper drawing of Folding Graphs and the new --outputformats command line option for PLCC, which allows selecting the graph output formats you want on the command line.

Some bug fixes have been submitted to the public SVN repo. They include:

PLCC:
- Folding graphs are drawn like protein graphs now (instead of using unfinished alternate representation which is still under development)
- Output graph formats can now be specified on the command line (new -O or --outputformats option)

VPG:
- The form to generate a DSSP file has the option to automatically delete temporary PDB files after the run
- New Help form (F1) which shows basic info on getting help for VPLG.... read more

The most important changes in this release are some improvements for VPG. A new form allows you to easily create a DSSP file from a PDB file, i.e., have the dsspcmbi program by Kabsch & Sander assign secondary structure information to the atom coordinates in the PDB file. Some fixes, rearranged menus and new keyboard shortcuts for many VPG features are also new.

A new version of VPLG has been released.

This version includes a number of bug fixes and improvements for the new VPG GUI. The most important change is that the PLCC working directory is now set properly. There also is more documentation on all the settings, implemented as tool tips. Instant input validation for all the form fields is also available now and invalid settings are marked in red. Some bug fixes and output changes for PLCC also made it into this release.... read more

A new version of VPLG has been released. This version has a number of small fixes for PLCC, but the important thing about it is the new graphical user interface. It can be used to download PDB and DSSP input files, create protein ligand graphs from them and view the resulting graphs. Here is a screenshot:

The source code in out SVN repo has been updated to revision 31. This version includes the new program VPG, which is a GUI for plcc.

A screenshot is available on the VPG wiki page.

Expect a new release which includes the GUI soon. I intend to submit some small bug fixes for PLCC before the release though.

A new version of VPLG has just been released. This version dramatically improves the interface to other software by adding support for saving protein graphs generated by VPLG in various standard graph file formats.

New features include:

• option to filter ligands based on their atom count, e.g., you can configure the program to include only ligands which have between n and m atoms. You can set the borders n and m in the PLCC configuration file using the plcc_I_lig_min_atoms and plcc_I_lig_max_atoms options. Setting the former to 1 and the latter to a value <0 (which are the defaults) means that all ligands are considered.
• changes under the hood, most notably usage of generics for the graph classes to unify them and make all of them extend a single base class.
• lots of new output formats to allow the usage of graphs generated by VPLG with other software:
  • GML: option to save the computed protein graphs to text files in Graph Modelling Language format (.gml files, see this report by Himsolt). The GML output is on by default and can be turned off by modifying the plcc_B_output_GML option in the VPLG config file. With GML support, you can now load graphs generated by VPLG in programs like yEd and Gephi.
  • TGF: option to save the computed protein graphs to text files in Trivial Graph Format format (.tgf files). This output is on by default and can be turned off by modifying the plcc_B_output_TGF option in the VPLG config file. Software supporting TGF includes the graph editor yEd.
  • DOT language: option to save the computed protein graphs to text files in DOT language format. This output is on by default and can be turned off by modifying the plcc_B_output_DOT option in the VPLG config file, it writes .gv files. This allows you to open the graphs with GraphViz and other software.... read more

The SVN repo here has been updated from our internal repo. This revision includes the option to save the computed protein graphs to text files in Graph Modelling Language format (.gml files, see this publication by Himsolt or this Wiki article for more info).... read more