About MPID-T2:The MHC-Peptide Interaction Database-TR version 2 (MPID-T2) is a new generation database for sequence-structure-function information on T cell receptor/peptide/MHC interactions. It contains all known crystal structures of TR/pMHC and pMHC complexes, with emphasis on the structural characterization of these complexes. MPID-T2 will facilitate the development of algorithms to predict whether a peptide sequence will bind to a specific MHC allele forming a pMHC agonist which will consequently be recognized by a particular TR leading to T cell activation for immune response. The database has been populated with data from the Protein Data Bank(PDB). The data from PDB is manually verified and classified, after which each structure is analysed for atomic interactions relevant to pMHC and TR/pMHC complexes. The intermolecular hydrogen bonds are calculated using the program HBPLUS, gap volume is pre-computed using the program SURFNET and change in interface area due to complex formation is calculated based on accessible surface area calculation performed by the NACCESS program for structures released until December 2006 and by the ICM program for structures released after December 2006. Gap index is calculated using the values for gap volume and interface area. Schematic diagrams of the pMHC and TR/pMHC interactions based on the plotting program LIGPLOT are also available.The peptide consensus patterns available in MPID-T2 are generated using the program WEBLOGO. MPID-T2 (November 2010 update) contains 415 entries from five MHC sources (Human:282, Murine:127, Rat:3, Chicken:2 and Monkey:1), spanning 56 alleles. 353 of which are pMHC structures and 62 TR/pMHC complexes. MHC-I (class I pMHC and TR/pMHC) complexes number 352 while 63 structures are from MHC-II (class II pMHC and TR/pMHC) complexes. On the whole, 327 entries are non-redundant (279 from MHC-I and 48 from MHC-II complexes). Among the TR/pMHC structures 50 are MHC-I and 11 are MHC-II structures. Included in this version are non-classical structures and complexes with non-standard residues. MPID-T2 is updated on a quaterly basis. To view the distribution graphically [click here]. To visualize the structural alignment you need Chime or Java plug-in for Jmol. MPID-T2 is best viewed using Internet Explorer. MPID-T2 Team:MPID-T2 is proudly brought to you by |