Abstract
A crucial step in designing of peptide vaccines involves the identification of B-cell epitopes. In past, numerous methods have been developed for predicting continuous B-cell epitopes, most of these methods are based on physico-chemical properties of amino acids. Presently, its difficult to say which residue property or method is better than the others because there is no independent evaluation or benchmarking of existing methods. In this study the performance of various residue properties commonly used in B-cell epitope prediction has been evaluated on a clean dataset. The dataset used in this study consists of 1029 non-redundant B cell epitopes obtained from Bcipep database and equally number of non-epitopes obtained randomly from SWISS-PROT database. The performance of each residue property used in existing methods has been computed at various thresholds on above dataset. The accuracy of prediction based on properties varies between 52.92% and 57.53%. We have also evaluated the combination of two or more properties as combination of parameters enhance the accuracy of prediction. Based on our analysis we have developed a method for predicting B cell epitopes, which combines four residue properties. The accuracy of this method is 58.70%, which is slightly better than any single residue property. A web server has been developed to predict B cell epitopes in an antigen sequence. The server is accessible from http://www.imtech.res.in/raghava/bcepred/.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Nicholson, B.H.: Experimental determination of immunogenic sites. In: Synthetic Vaccines, pp. 137–168. Published by Blackwell scientific publications, London (1994)
Flower, D.R.: Towards in silico prediction of immunogenic epitopes. TRENDS in immunology 24, 667–674 (2003)
Pellequer, J.L., Westhof, E., Regenmortel, M.H.V.: Predicting location of continuous epitopes in proteins from their primary structures. Methods in enzymology 203, 176–201 (1991)
Hopp, T.P., Woods, R.K.: Predictions of protein antigenic determinants from amino acid sequences. Proc. Natl. Acad. Sci. USA. 78, 3824–3828 (1981)
Parker, J.M.D., Guo, D., Hodges, R.S.: New hydrophilicity scale derived from highperformance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. Biochemistry 25, 5425–5432 (1986)
Karplus, P.A., Schulz, G.E.: Prediction of chain flexibility in proteins: a tool for the selection of peptide antigen. Naturwissenschaften 72, 212–213 (1985)
Emini, E.A., Hughes, J.V., Perlow, D.S., Boger, J.: Induction of hepatitis A virusneutralizing antibody by a virus-specific synthetic peptide. J. Virol. 55, 836–839 (1985)
Kolaskar, A.S., Tongaonkar, P.C.: A semi-emperical method for prediction of antigenic determinants on protein antigens. FEBS 276, 172–174 (1990)
Pellequer, J.-L., Westhof, E., Regenmortel, M.H.V.: Correlation between the location of antigenic sites and the prediction of turns in proteins. Immunol. Lett. 36, 83–99 (1993)
Pellequer, J.L., Wasthof: PREDITOP: A program for antigenicity prediction. J. Mol. Graphics. 11, 204–210 (1993)
Alix, A.J.: Predictive estimation of protein linear epitopes by using the program PEOPLE. Vaccine 18, 311–314 (1999)
Odorico, M., Pellequer, J.L.: BEPITOPE: predicting the location of continuous epitope and patterns in proteins. J. Mol. Recognit. 16, 20–22 (2003)
Saha, S., Bhasin, M., Raghava, G.P.S.: Bcipep: A database of B cell epitopes (2004) (submitted)
Bairoch, A., Apweiler, R.: The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45–48 (2000)
Janin, J., Wodak, S.: Conformation of amino acid side-chains in proteins. J. Mol. Biol. 125, 357–386 (1978)
Ponnuswamy, P.K., Prabhakaran, M., Manavalan, P.: Hydrophobic packing and spatial arrangements of amino acid residues in globular proteins. Biochim. Biophys. Acta. 623, 301–316 (1980)
Deleo, J.M.: Proceedings of the Second International Symposium on Uncertainity Modelling and Analusis, pp. 318–325. IEEE. Computer Society Press, College Park (1993)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Saha, S., Raghava, G.P.S. (2004). BcePred: Prediction of Continuous B-Cell Epitopes in Antigenic Sequences Using Physico-chemical Properties. In: Nicosia, G., Cutello, V., Bentley, P.J., Timmis, J. (eds) Artificial Immune Systems. ICARIS 2004. Lecture Notes in Computer Science, vol 3239. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30220-9_16
Download citation
DOI: https://doi.org/10.1007/978-3-540-30220-9_16
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-23097-7
Online ISBN: 978-3-540-30220-9
eBook Packages: Springer Book Archive