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, e.g. usually alpha helices and beta sheets) or ligand molecules while the edges model contacts and spatial relations between them.
This is the Visualization of Protein Ligand Graphs (VPLG) software package. It includes several applications written in Java and Perl. See the doc/ subdirectory of the release for help with the programs. VPLG was written by Tim Schaefer at the Molecular Bioinformatics Group of Ina Koch at Goethe-University Frankfurt, Germany. It is based and earlier work by Ina Koch and Patrick May. See http://
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trunk series is the current focus of development.
