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Contents:

General Information
  • PTGL Members
    List of people associated with the PTGL:

    Prof. Dr. Ina Koch
    Beuth University of Applied Sciences Berlin
    FB VI
    Seestr.64
    13347 Berlin
    Germany

    Max Planck Institute for Molecular Genetics
    Compuational Molecular Biology
    Ihnestr. 73
    14195 Berlin
    Germany

    		 Phone  +49 +30 4504-3972
    Fax      +49-30-4504-3959
    e-mail:  ina.koch (at) tfh-berlin.de
    http://www.beuth-hochschule.de/people/detail/468


    Phone  +49 +30 8413-1168
    e-mail:  ina.koch (at) molgen.mpg.de
    http://www.molgen.mpg.de/~koch_i
    Dr. Patrick May
    Max Planck Institute of Molecular Plant Physiology
    Am Muehlenberg 1
    14476 Potsdam-Golm
    Germany

    		 Phone  +49 331 567-8615
    e-mail:  may (at) mpimp-golm.mpg.de
    http://bioinformatics.mpimp-golm.mpg.de/group-members/patrick-may
    Dr. Thomas Steinke
    Zuse Institute Berlin
    Computer Science Research
    Takustr. 7
    14195 Berlin, Germany

    		 e-mail:  steinke (at) zib.de

PTGL WWW User Guides
  • What is PTGL ?
    Documentation of PTGL, description of the graph types, linear notations, and how to link to PTGL.
  • SearchKey
    Documentation for the SearchKey query capability including general operation, lists of attributes and the syntax for the formulation of complex queries
  • SearchFields
    A description of the more advanced query capabilities available within the SearchFields interface
  • SearchMotifs
    A description of the query for protein structure motifs SearchMotifs interface
  • SearchList
    A description of the more advanced query capabilities for two or more PTGL-IDs in the SearchList interface
  • SearchSequence
    A description of the BLAST sequence search in the SearchSequence interface

File Formats and Standards

PTGL PostgreSQL Database

News and Discussion

  • 16-Juni-2009: Relaunch on ptgl.zib.de, update PDB,SCOP,CATH
  • 18-Juni-2009: PDBsum links added
  • 14-August-2009: full database update to the newest PDB version
  • 12-November-2009: Nucleic Acids Research Database issue 2010 paper online: 10.1093/nar/gkp980.

Publications

  • 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.