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Published on: July 19, 2024
PTGL: extension to graph-based topologies of cryo-EM data for large protein structures
Jan Niclas Wolf1, Marcus Keßler1, Jörg Ackermann1
1Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, Johann Wolfgang Goethe-University Frankfurt am Main, 60325 Frankfurt am Main, Germany.
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.
