Summary
In this chapter, two prediction servers of linear B-cell epiotpes have been described; (i) BcePred, based on physico-chemical properties that include hydrophilicity, flexibility/mobility, accessibility, polarity, exposed surface, turns, and antigenicity and ii) ABCpred, based on recurrent neural network. Both of the servers assist in locating linear epitope regions in a protein.
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References
Saha, S. and Raghava, G.P.S. (2004) BcePred: prediction of continuous B-cell epitopes in antigenic sequences using physico-chemical properties. In Artificial Immune Systems, Nicosia, G., Cutello, V., Bentley, P.J., and Timis, J., (eds.) ICARIS, LNCS 3239, Springer. Publishers, pp. 197–204.
Hopp, T.P. and Woods, R.K. (1981) Predictions of protein antigenic determinants from amino acid sequences. Proc. Natl. Acad. Sci. U.S.A. 78, 3824–3828.
Karplus, P.A. and Schulz, G.E. (1985) Prediction of chain flexibility in proteins: a tool for the selection of peptide antigen. Naturwissenschaften 72, 212–213.
Emini, E.A., Hughes, J.V., Perlow, D.S. and Boger, J. (1985) Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J. Virol. 55, 836–839.
Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P. (1980) Hydrophobic packing and spatial arrangements of amino acid residues in globular proteins. Biochim. Biophys. Acta. 623, 301–316.
Janin, J. and Wodak, S. (1978) Conformation of amino acid side-chains in proteins. J. Mol. Biol. 125, 357–386.
Pellequer, J.-L., Westhof, E. and Regenmortel, M.H.V. (1993) Correlation between the location of antigenic sites and the prediction of turns in proteins. Immunol. Lett. 36, 83–99.
Kolaskar, A.S. and Tongaonkar, P.C. (1990) A semi-emperical method for prediction of antigenic determinants on protein antigens. FEBS Lett., 276, 172–174.
Blythe, M.J. and Flower, D.R. (2005) Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci., 14, 246–248.
Saha, S., Bhasin, M. and Raghava, G.P.S. (2005) Bcipep: a database of B-cell epitopes. BMC Genomics, 6, 79
Saha, S. and Raghava, G.P.S. (2006) Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. PROTEINS: Structure, Functions, and Bioinformatics 65, 40–48.
Zell, A. and Mamier, G. (1997) Stuttgart Neural Network Simulator version 4.2. University of Stuttgart, Stuttgart, Germany.
Acknowledgments
We acknowledge the financial support from the Council of Scientific and Industrial Research (CSIR) and Department of Biotechnology (DBT), Govt. of India.
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© 2007 Humana Press Inc.
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Saha, S., Raghava, G.P. (2007). Prediction Methods for B-cell Epitopes. In: Flower, D.R. (eds) Immunoinformatics. Methods in Molecular Biology™, vol 409. Humana Press. https://doi.org/10.1007/978-1-60327-118-9_29
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DOI: https://doi.org/10.1007/978-1-60327-118-9_29
Publisher Name: Humana Press
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