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.
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The new Protein Topology Graph Library web server.
Schäfer T, Scheck A, Bruneß D, May P, Koch I.
Bioinformatics. 2015 Oct 6. pii: btv574.