Visualization of Protein-Ligand Graphs / Blog: Recent posts

Revision 21 has been added to the code in our SVN. The changes include a new 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. This was a suggestion of a reviewer of the paper.... read more

A new version of VPLG has been released. It comes with many fixes and some new features for both splitpdb and plcc:

• support for deleting a protein from the database
• splitpdb now also supports gzipped input PDB files and can also write gzipped output files
• computation of a spatial vertex ordering of a graph if possible for the graph
• based on this vertex ordering, the KEY notation from the Protein Topology Graph Library can also be computed
• database layout changes and fixes
• work on similarity methods for protein graphs (--similar command line option, similarity src package)
• changed the values of some default settings inthe cfg file... read more

The source code has been updated from our internal repo and the repo here at SF is now at revision 18. Many fixes and improvements everywhere. Implementations of some classical algorithms from the field of bioinformatics (Needleman-Wunsch, Smith-Waterman) have been added. They are used in the new similarity methods that are intended to allow searching for graphs in the database which are similar to a given template graph in the future. Other major changes include code for spatial ordering of SSEs in graphs. Minor changes to DB layout, changed some default settings, etc. ... read more

The source code has been updated to r15 in the SVN. New features include the computation of a spatial vertex ordering of a graph if supported for the graph, i.e., the graph is connected and has no vertex with degree > 2. Based on this vertex ordering, the KEY notation from the Protein Topology Graph Library can also be computed.

The code in the SVN has been updated to r13. The new version of PLCC has support for deleting a protein from the database. (You can ignore this if you don't use the database functionality of PLCC).

Updating a protein in the database, e.g. because a newer version of the PDB file becomes available, was already supported before this - but deleting a protein was not. This is necessary when a PDB file becomes deprecated though.... read more

The Wiki has been updated, it now has a new page which explains how VPLG works, i.e., how the protein ligand graph is computed from the atom coordinates and the SSE data in the PDB and DSSP files.

The documentation in the Wiki has been updated. It now includes a section that explains the different graph types of VPLG and comes with many screenshots.

The SVN repo has been updated. The splitpdb program now supports gzipped input PDB files and can also write gzipped output files. Example:

java -jar splitpdb.jar 1blr.pdb.gz --zipped-input --model 1 --zip-output -o 1blr_model1.pdb

This command will read the gzipped input file 1blr.pdb.gz, extract all general data and the data on the first model and write the output to the gzipped output archive 1blr_model1.pdb.gz. This archive will contain a single text file named 1blr_model1.pdb.

VPLG version 2012_02_21 has been released. This version fixes bitmap output support (-m), adds support for gzipped input files and fixes some database-related security issues. The database structure has also been changed slightly and output files can now be written to a directory tree similar to the PDB directory structure to avoid problems with thousands of output files in a single directory (-k).

The source code in the SVN has been updated to revision 9.
Changes:

• fixed PNG support, added support for TIF and JPG (-m PNG|TIF|JPG|SVG), this is done with the Apache Batik library
• SVG is default and always drawn
• DB security fixes, using prepared statements for all functions which depend on user input now
• new output tree feature (-k)
• support for gzipped input PDB and DSSP files (--gz-pdbfile and --gz-dsspfile)
• drawing legends under the images is now possible (but can be disabled in config file)... read more