PTGL: extension to graph-based topologies of cryo-EM data for large protein structures

Abstract

Summary: We provide a software to describe the topology of large protein complexes based mainly on cryo-EM data and stored as macromolecular Crystallographic Information Files (mmCIFs) in the PDB. The software extends the Protein Topology Graph Library and implements an efficient file parser to analyze mmCIFs. The extended Protein Topology Graph Library includes a graph-based representation of the topology of protein complexes on the supersecondary and quaternary structure level. The library holds topology graphs of 151 837 PDB files; 921 of them are large structures. The abstraction of protein structure complexes to undirected labeled graphs enables classification and comparison of large protein complexes on quaternary structure level.

Availability and implementation: Online access at http://ptgl.uni-frankfurt.de. Source code in Java under GNU public license 2.0 at https://github.com/MolBIFFM/vplg.

Supplementary information: Supplementary data are available at Bioinformatics online.