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Applied Bioinformatics

, Volume 5, Issue 2, pp 111–114 | Cite as

MPID-T

Database for Sequence-Structure-Function Information on T-Cell Receptor/Peptide/MHC Interactions
  • Joo Chuan Tong
  • Lesheng Kong
  • Tin Wee Tan
  • Shoba RanganathanEmail author
Database Note

Abstract

Normal adaptive immune responses operate under major histocompatibility complex (MHC) restriction by binding to specific, short antigenic peptides and presenting them to appropriate T-cell receptors (TcRs). Sequence-structure-function information is critical in understanding the principles governing peptide/MHC (pMHC) and TcR/pMHC recognition and binding. A new database for sequence-structure-function information on TcR/pMHC interactions, MHC-Peptide Interaction Database version T (MPID-T), is now available with the latest available Protein Data Bank (PDB) data and interaction parameters on TcR/pMHC complexes. MPID-T is a manually curated MySQL® database containing experimentally determined structures of 187 pMHC complexes and 16 TcR/pMHC complexes available in the PDB. Each structure is manually verified, classified, and analysed for intermolecular interactions (i) between the MHC and its corresponding bound peptide and (ii) between TcR and its bound pMHC complex where TcR structural information is available. The MPID-T database retrieval system has precomputed interaction parameters that include solvent accessibility, hydrogen bonds, gap volume and gap index. Structural visualisation of the TcR/pMHC complex, pMHC complex, MHC or the bound peptide can be performed using freely available graphics applications such as MDL® Chime or RasMol, while structural alignment (based on MHC class and peptide length) can be viewed using the Jmol molecular viewer or an MDL® Chime-compatible web browser client. MPID-T contains structural descriptors for in-depth characterisation of TcR/pMHC and pMHC interactions. The ultimate purpose of MPID-T is to enhance the understanding of the binding mechanism underlying TcR/pMHC and pMHC interactions by mapping the TcR footprint on the MHC and its bound peptide, as this eventually determines T-cell recognition and binding.

Keywords

Major Histocompatibility Complex Protein Data Bank Major Histocompatibility Complex Allele Protein Data Bank Entry Major Histocompatibility Complex Binding 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

The authors have no conflicts of interest that are directly relevant to the content of this article.

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Copyright information

© Adis Data Information BV 2006

Authors and Affiliations

  • Joo Chuan Tong
    • 1
    • 2
  • Lesheng Kong
    • 1
  • Tin Wee Tan
    • 1
  • Shoba Ranganathan
    • 3
    • 1
    Email author
  1. 1.Department of Biochemistry, Yong Loo Lin School of MedicineNational University of SingaporeSingapore
  2. 2.Institute for Infocomm ResearchSingapore
  3. 3.Department of Chemistry and Biomolecular Sciences, and Biotechnology Research InstituteMacquarie UniversitySydneyAustralia

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