Journal of Molecular Modeling

, Volume 16, Issue 7, pp 1283–1289

TollML: a database of toll-like receptor structural motifs

  • Jing Gong
  • Tiandi Wei
  • Ning Zhang
  • Ferdinand Jamitzky
  • Wolfgang M. Heckl
  • Shaila C. Rössle
  • Robert W. Stark
Original Paper

Abstract

Toll-like receptors (TLRs) play a key role in the innate immune system. TLRs recognize pathogen-associated molecular patterns and initiate an intracellular kinase cascade to induce an immediate defensive response. During recent years TLRs have become the focus of tremendous research interest. A central repository for the growing amount of relevant TLR sequence information has been created. Nevertheless, structural motifs of most sequenced TLR proteins, such as leucine-rich repeats (LRRs), are poorly annotated in the established databases. A database that organizes the structural motifs of TLRs could be useful for developing pattern recognition programs, structural modeling and understanding functional mechanisms of TLRs. We describe TollML, a database that integrates all of the TLR sequencing data from the NCBI protein database. Entries were first divided into TLR families (TLR1-23) and then semi-automatically subdivided into three levels of structural motif categories: (1) signal peptide (SP), ectodomain (ECD), transmembrane domain (TD) and Toll/IL-1 receptor (TIR) domain of each TLR; (2) LRRs of each ECD; (3) highly conserved segment (HCS), variable segment (VS) and insertions of each LRR. These categories can be searched quickly using an easy-to-use web interface and dynamically displayed by graphics. Additionally, all entries have hyperlinks to various sources including NCBI, Swiss-Prot, PDB, LRRML and PubMed in order to provide broad external information for users. The TollML database is available at http://tollml.lrz.de.

Keywords

TollML Toll-like receptor Leucine-rich repeats XML database Homology modeling 

Supplementary material

894_2009_640_MOESM1_ESM.pdf (33 kb)
Supplementary File 1Document type definition (DTD) file of TollML (PDF 33 kb)
894_2009_640_MOESM2_ESM.pdf (52 kb)
Supplementary File 2XML Stylesheet (XSLT) of a TollML entry (PDF 51 kb)

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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Jing Gong
    • 1
    • 2
  • Tiandi Wei
    • 1
    • 2
  • Ning Zhang
    • 3
  • Ferdinand Jamitzky
    • 1
    • 4
  • Wolfgang M. Heckl
    • 1
    • 5
    • 6
  • Shaila C. Rössle
    • 2
  • Robert W. Stark
    • 1
    • 2
  1. 1.Center for NanoscienceLudwig-Maximilians-Universität MünchenMunichGermany
  2. 2.Department of Earth and Environmental SciencesLudwig-Maximilians-Universität MünchenMunichGermany
  3. 3.Department of InformaticsLudwig-Maximilians-Universität MünchenMunichGermany
  4. 4.Leibniz Supercomputing CentreGarchingGermany
  5. 5.Deutsches MuseumMunichGermany
  6. 6.TUM School of EducationTechnische Universität MünchenMunichGermany

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