Publications related to PTGL

Here is a list of all publications related to the PTGL and its underlying software, PTGLtools (formerly labeled VPLG). If you use our web server or software, please consider citing us.

• Wolf JN, Keßler M, Ackermann J, Koch I (2020). PTGL: extension to graph-based topologies of cryo-EM data for large protein structures. Bioinformatics. (DOI 10.1093/bta706 at Oxford University Press).
• Koch I and Schäfer T (2018). Protein super-secondary structure and quaternary structure topology: theoretical description and application. Current opinions in structural biology, 50, 134-143
• Schäfer T, Scheck A, Bruneß D, May P, Koch I (2015). The new protein topology graph library web server. Bioinformatics. (btv574 at oxfordjournals.org).
• Koch I, Kreuchwig A, May P (2013). Hierarchical representation of supersecondary structures using a graph-theoretical approach. Journal of Methods in molecular biology 2013;932:7-33. (/pubmed/22987344).
• Schäfer T, May P, Koch I (2012). Computation and Visualization of Protein Topology Graphs Including Ligand Information. German Conference on Bioinformatics 2012; 108-118. (DROPS).
• May P, Kreuschwig A, Steinke T, Koch I (2009). PTGL - a database for secondary structure-based protein topologies. Nucleic Acids Research, 10.1093/nar/gkp980 (Database issue 2010).
• May P, Barthel S, Koch I (2004). PTGL - Protein Topology Graph Library. Bioinformatics 20(17):3277-3279.
• Koch I, Lengauer T (1997) Detection of distant structural similarities in a set of proteins using a fast graph-based method. Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology, 21.-26 Juni, Halkidiki, Greece AAAI Press, California. eds. T. Gaasterland, P. Karp, K. Karplus, C. Ouzounis, C. Sander, A. Valencia:167-187.
• Koch I, Wanke E, Lengauer T (1996) An algorithm for finding maximal common subtopologies in a set of proteins. Journal of Computational Biology 3(2):289-306.
• Koch I, Kaden F, Selbig J (1992) Analysis of Protein Sheet Topologies by Graph Theoretical Methods. Proteins: Structure, Function, and Genetics 12:314--323.
• Kaden K, Koch I, Selbig J (1990) Knowledge-based prediction of protein structures. Journal of Theoretical Biology 147(1):85-100.