Extension of protein topologies by ligand information: computation and visualization

The Protein Topology Graph Library (PTGL) is a database of protein topologies that provides a web interface to compare and visualize protein folds based on the super-secondary structure. It uses a graph-based protein model related to earlier work by Koch et al.: the vertices of the protein graph represent the secondary structure elements
(SSEs) α-helix and β-sheet while the edges model contacts and spatial relations between these SSEs. Similarity between proteins is defined via common substructures in their protein graphs. In this work, the graph model has been extended to include ligand information and the new software VPLG that computes and visualizes the resulting protein graphs has been developed. VPLG reads and writes protein graphs in a custom text-based format, saves the resulting images in PNG or SVG format and comes with database support.