title: MPID-T: database for sequence-structure-function information on T-cell receptor/peptide/MHC interactions.
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.
  
  
  BACKGROUND
  The MPID-T database retrieval system is available at http://surya.bic.nus.edu.sg/mpidt
  
  
  BACKGROUND
  Joo Chuan Tong (jctong@i2r.a-star.edu.sg).
authors.affiliation: Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore Institute for Infocomm Research, Singapore. jctong@i2r.a-star.edu.sg
authors.forename: Joo Chuan
authors.initials: JC
authors.lastname: Tong
authors.forename: Lesheng
authors.initials: L
authors.lastname: Kong
authors.forename: Tin Wee
authors.initials: TW
authors.lastname: Tan
authors.forename: Shoba
authors.initials: S
authors.lastname: Ranganathan
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030541:Databases, Genetic; D030562:Databases, Protein; D006649:Histocompatibility Antigens / Q000737:chemistry; D006801:Humans; D006860:Hydrogen Bonding; D020407:Internet; D008285:Major Histocompatibility Complex; D010455:Peptides / Q000737:chemistry*; D011485:Protein Binding; D011948:Receptors, Antigen, T-Cell / Q000737:chemistry*; D013329:Structure-Activity Relationship
chemical_list: D006649:Histocompatibility Antigens; D010455:Peptides; D011948:Receptors, Antigen, T-Cell