Computation and visualization of protein topology graphs including ligands

Ligand information is of great interest to understand protein function. Protein structure topology can be modeled as a graph, with secondary structure elements as vertices and spatial contacts between them as edges. Meaningful representations of such graphs in 2D are required for the visual inspection, comparison and analysis of protein folds, but their automatic visualization is still challenging. We present an approach which solves this task, supports several graph types and includes ligands. Our method generates a mathematically unique representation and high-quality 2D plots of the secondary structure of proteins based on a protein ligand graph. This graph is computed from 3D atom coordinates in PDB files and the corresponding SSE assignments of the DSSP algorithm. The VPLG software enables rapid visualization of protein structures and exports graphs in various standard file formats for further analysis. It is available under an open source license at http://vplg.sourceforge.net/.