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MHCBN

http://webs.iiitd.edu.in/raghava/mhcbn/

Bhasin, M., Singh, H., Raghava, G. P. S.

Indraprastha Institute of Information Technology Okhla Phase 3, New Delhi, India

Contact   raghava@iiitd.ac.in

Database Description

The MHCBN is a comprehensive database of Major Histocompatibility Complex (MHC) binding and non-binding peptides. It is a curated database where the entries are compiled from published literature. Each entry in database consists the following information i) peptide sequence ii) MHC-peptide binding strength iii) potential of T-cell activation iv) sequence & structure of MHC molecule & associated proteins and v) internal & external hypertext data links. The MHCBN have number of online web tools for the analysis and retrieval of data from the database. These tools allow users to i) search the relevant information, ii) perform BLAST search against antigens and MHC sequences, iii) create allele specific data set and iv) submit data online. The server provides option to map the peptides in MHCBN database on a query protein sequence. This option would be very useful in locating the MHC binders/non-binders and T-cell epitopes in user?s antigen sequence. The latest version of MHCBN contains 16598 entries that include 14816 binders, 1782 non-binders and 5456 T-cell epitope entries. The database also maintains i) 2825 sequences & 676 structures of proteins having matching peptide, ii) 928 publication references, iii) 91 structure of MHC proteins and iv) 1457 sequence of MHC proteins. The server provides the hypertext link to major databases like SWISSPROT, PDB, IMGT/HLA-DB, PubMed and ENTREZ. The MHCBN database and its applications are freely available at http://webs.iiitd.edu.in/raghava/mhcbn/.

Acknowledgements

Authors are thankful to CSIR and Department of Biotechnology (DBT), Govt. of India, for financial assistance.

REFERENCES

1. Sandberg,J.K., Leandersson,A.C.,Devito,C.,Kohleisen,B., Erfle,V., Achour,A., Levi,M., Schwartz,S., Karre,K., Wahren,B. and Hinkula,J. (2000) Human immunodeficiency virus type 1 Nef epitopes recognized in HLA-A2 transgenic mice in response to DNA and peptide immunization. Virology, 273, 112-9.
2. Brusic,V., Rudy,G. and Harrison,L.C. (1998) MHCPEP, a database of MHC-binding peptides: update 1997. Nucleic Acids Res., 26, 368-71.
3. Schonbach,C., Koh,J.L., Sheng,X., Wong,L. and Brusic,V. (2000) FIMM, a database of functional molecular immunology. Nucleic Acids Res., 28, 222-4.
4. Robinson,J., Waller,M.J., Parham,P., Bodmer,J.G. and Marsh,S.G. (2001) IMGT/HLA Database--a sequence database for the human major histocompatibility complex. Nucleic Acids Res., 29, 210-3.
5. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
6. Altschul,S.F., Madden,T.L., Sch‰ffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
7. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-80.
8. Brown,N.P., Leroy,C. and Sander,C. (1998) MView: a web-compatible database search or multiple alignment viewer. Bioinformatics, 14, 380-1.

Category   Protein Databases