Visualization of Protein Ligand Graphs (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. The graphs can be visualized, written to a database, and saved in a text-based file format.
|Tags||Bioinformatics Protein structure Graph theory Ligand Protein topology Visualization|
|Licenses||Open Software Artistic|
|Operating Systems||platform independent (Java)|
Release Notes: 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 metadata (e.g. species) to exported graphs in comments (for export formats that support comments but no graph metadata).
Release Notes: 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.
Release Notes: This version comes with many fixes and some new features for both splitpdb and plcc: support for deleting a protein from the database; splitdb support for gzipped input PDB files and writing gzipped output files; database layout changes and fixes; and work on similarity methods for protein graphs. It adds 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.