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MPID-T2


NAR Molecular Biology Database Collection entry number 107
Ranganathan, S.1, Govindarajan, K.R.1, Kangueane, P.2, Tan, T.W.1
1Bioinformatics Centre & Dept. of Biochemistry National University of Singapore Singapore 119260
2Bioinformatics Centre National University of Singapore Singapore 119260

Database Description

MPID-T2 (http://biolinfo.org/mpid-t2/) is a highly curated database for sequence-structure-function information on MHC-peptide interactions. It contains all structures of major histocompatibility complex proteins (MHC) containing bound peptides, with emphasis on the structural characterization of these complexes. Database entries have been grouped into fully referenced redundant and non-redundant categories. The MHC-peptide interactions have been presented in terms of a set of sequence and structural parameters representative of molecular recognition. MPID will facilitate the development of algorithms to predict whether a query peptide sequence will bind to a specific MHC allele. Currently, there are five data classes in MPID: MHC-peptide complexes, MHC, Peptides, Interactions and References. The database has a full set of search tools for the extraction of information based on complex queries and the results are presented as lists. Hyperlinks to sequence databases specific to MHC-peptide interactions as well as to literature and relevant structural databases have been provided. The annual growth of MPID data as well as the patterns of conservation observed among the peptides within MPID are presented graphically. MPID data has been sorted primarily on the basis of MHC Class, followed by organism (MHC source), next by allele type and finally by the length of peptide in the binding groove (peptide residues within 5 Ã… of the MHC). Redundancy has been removed by selecting the best structure from each group, on the basis of lowest resolution and completeness of structural information on the binding groove. Several PDB entries contain multiple protein chains of both the MHC and the peptide. The first MHC chain and its associated peptide alone are stored in MPID in the form of a single MHC-peptide complex, with their relevant chain identifiers. The coordinates corresponding to the MHC protein chain (or chains in the case of Class II), the peptide and a single MHC-peptide complex are dynamically extracted from each PDB entry and served in a format suitable for visualization using freely available viewers. Data on inter-molecular hydrogen bonds, gap volume and gap index available in MPID are pre-computed and the interface area due to complex formation is calculated based on accessible surface area calculations. Schematic diagrams representing MHC-peptide interactions are also available in MPID. The entire dataset including coordinates of single MHC-peptide complexes can be downloaded. The available MHC-peptide databases have addressed sequence information as well as binding (or the lack thereof) of peptide sequences but the structural dimensionality (i.e. sequence-structure-function) has been missing. MPID is out attempt to providing this vital information. At present MPID (release 1.0 July 2001; based on PDB update 1 August 2001) contains 72 entries from three MHC sources: (human: 46, murine: 25 and rat: 1), spanning 20 alleles with 59 peptide ligands. Class I MHC-peptide complexes number 56 while 16 structures are from Class II MHC. On the whole, 59 entries are non-redundant (46 from Class I and 13 from Class II MHC-peptide complexes.

Acknowledgements

This work was partially funded by the National Science and Technology Board (NSTB), Singapore and the National University of Singapore (NUS). K.R.G. gratefully acknowledges the award of an NSTB research scholarship from NUS.

References

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