Summary
One of the major challenges in the field of subunit vaccine design is to identify the antigenic regions in an antigen, which can activate B cell. These antigenic regions are called B-cell epitopes. In this chapter, we describe how to use Bcipep, which is a database of experimentally determined linear B-cell epitopes of varying immunogenicity collected from literature and other publicly available databases. The current version of Bcipep database contains 3,031 entries that include 763 immunodominant, 1,797 immunogenic, and 471 null-immunogenic epitopes. The database provides a set of tools for analysis and extraction of data that includes keyword search, peptide mapping, and BLAST search. The database is available http://www.imtech.res.in/raghava/bcipep/.
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References
Saha, S., Bhasin, M. and Raghava, G.P.S. (2005) Bcipep: a database of B-cell epitopes. BMC Genomics 6(1):79
Saha, S., Bhasin, M. and Raghava, G.P.S. (2005) Bcipep. Nucleic Acids Res. (Online; http://www3.oup.co.uk/nar/database/summary/642/).
Blythe, M.J., Doytchinova, I.A. and Flower, D.R. (2002) JenPep: a database of quantitative functional peptide data for immunology. Bioinformatics 18: 434–439.
Korber, B., Brander, C., Haynes, B., Koup, R., Kuiken, C., Moore, J., Walker, B. and Watkins, D. (2002) HIV monoclonal antibodies. In HIV Molecular Immunology 2001. Published by Theoretical Biology and Biophysics group T-10, Mail Stop K710 Los Alamos national Laboratory, Los Alamus, New Mexico, IV-B-1–IV-B-278.
Bhasin, M., Singh, H. and Raghava, G.P.S. (2003) MHCBN: a comprehensive database of MHC binding and non-binding peptides. Bioinformatics 19(5): 665–666.
Wheller, D.L., Church, D.M., Lash, A.E., Leipe, D.D., Madden, T.L., Pontius, J.U., Schuler, G.D., Schriml, L.M., Tatusova, T.A., Wagner, L. and Rapp, B.A. (2002) Database resources of National Center for Biotechnology Information: 2002 update. Nucleic Acids Res. 30: 13–16.
Bairoch, A. and Apweiler, R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28: 45–48.
Westbrook, J., Feng, Z., Jain, S., Bhat, T.N., Thanki, N., Ravichandran, V., Gilliland, G.L., Bluhm, W.F., Weissig, H., Greer, D.S., Bourne, P.E. and Berman, H.M. (2002) The Protein Data Bank: unifying the archive. Nucleic Acids Res. 30: 245–248.
Acknowledgments
We acknowledge the financial support from the Council of Scientific and Industrial Research (CSIR) and Department of Biotechnology (DBT), Government of India.
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Saha, S., Raghava, G.P. (2007). Searching and Mapping of B-Cell Epitopes in Bcipep Database. In: Flower, D.R. (eds) Immunoinformatics. Methods in Molecular Biology™, vol 409. Humana Press. https://doi.org/10.1007/978-1-60327-118-9_7
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DOI: https://doi.org/10.1007/978-1-60327-118-9_7
Publisher Name: Humana Press
Print ISBN: 978-1-58829-699-3
Online ISBN: 978-1-60327-118-9
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