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Reseach Article
Computational Methods in Linear B-cell Epitope Prediction
| International Journal of Computer Applications |
| Foundation of Computer Science (FCS), NY, USA |
| Volume 63 - Number 12 |
| Year of Publication: 2013 |
| Authors: Kavitha K V, Saritha R, Vinod Chandra S S |
10.5120/10520-5498
|
Kavitha K V, Saritha R, Vinod Chandra S S . Computational Methods in Linear B-cell Epitope Prediction. International Journal of Computer Applications. 63, 12 ( February 2013), 28-32. DOI=10.5120/10520-5498
Abstract
Immune systems protect the body from foreign molecules known as antigens. It has great pattern recognition capability that may be used to distinguish between foreign cells entering the body (non- self or antigen) and the body cells (self). Any substance like proteins, polysaccharides, lipoproteins, polypeptides, nucleoproteins and nucleic acids that can induce the immune system to produce a corresponding antibody is called an antigen. This ability of antigen is called antigenicity. That portion of the antigen which can bind with the antigen binding site of the antibody is called B-cell epitope or antigenic determinant. B-cell epitopes can be linear or conformational. These epitopes play a vital role in the development of peptide vaccines, in diagnosis of diseases, immune based cancer therapies and also for allergy research. Since experimental methods of identifying epitopes are costly and time consuming, computational methods for prediction are desirable. This paper reviews various approaches like amino acid scale based methods and machine learning methods used for the prediction of linear B-cell epitopes.
References
- Parham P. The Immune System, 2nd edition, Garland Science Publishing, NewYork, NY, 2005.
- Li J, Y. A. Zhang, H. Boshra, A. E. Gelman, S. LaPatra,,L. Tort and J. O. Sunyer. "B lymphocytes from early vertebrates have potent phagocytic and microbicidal abilities". Nature Immunology vol 7, pp 1116–1124.
- Janeway, C. A. , Jr. ; Travers, P. ; Walport, M. ; and Shlomchik. Immunobiology, 5th edition, Garland Science Publishing, NewYork, NY, 2001.
- R. Ahmed and J. Sprent, "Immunological Memory", The Immunologist, vol 7, pp. 23-26, 1999.
- L . N. D. Castron and F. J. V. Zuben, "Artificial Immune Systems Part I: Basic theory and applications", Technical Report TR-DCA 01/99, Dec 1999.
- J. Greenbaum, P. Andersen, M. Blythe, H. Bui, R. Cachau,J. Crowe M. Davies, A. Kolaskar, O. Lund, S. Morrison, et al. " Towards a consensus on datasets and evaluation metric for developing B-cell epitope prediction tools". Journal of Molecular Recognition, vol 20, pp 75–82, 2007.
- Y. EL-Manzalawy and V. Honavar, "Recent advances in B-cell epitope prediction methods", Immunome Research, vol 6, Nov 2010.
- T. P. Hopp and YK. R. Woods, "Prediction of protein antigenic determinants from amino acid sequences" PNAS, vol 78, pp 3824-3828, 1981.
- J. M. Parker, D. Guo, R. S. Hodges, "New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray derived accessible sites", Biochemistry, vol 25, pp 5425-5432, 1986.
- P. A. Karplus, and G. E. Schulz, "Prediction of chain flexibility in proteins – a tool for the selection of peptide antigens", Naturwissenschaft, vol 72, pp 212-213, 1985.
- Yemini, J. Hughes, D. Perlow and J. Boger, "Induction of hepatitis A virus neutralizing antibody by a virus-specific synthetic peptide. " Journal of Virology, vol55, pp 836-839, 1985.
- Janin, J. and Wodak, S. : Conformation of amino acid side-chains in proteins. Journal of Molecular Biology, vol 125, pp 357-86, 1978.
- P. Y. Chou and G. D. Fasman, "Prediction of secondary structure of proteins from amino acid sequences", Biochemistry, vol 47, pp 145–148, 1978.
- A. S. Kolaskar, P. C. Tongaonkar,,"A semi-empirical method for prediction of antigenic determinants on protein antigens", FEBS Lett,vol 276,pp172-174,1990
- J. Pellequer, E. Westhof and M. Van Regenmortel, "Correlation between the location of antigenic sites and the prediction of turns in proteins". Immunology, vol36, pp 83–99, 1993.
- A. Alix, "Predictive estimation of protein linear epitopes by using the program PEOPLE", Vaccine, vol 18, pp 311-14, 1999.
- M. Odorico, and J. Pellequer, "BEPITOPE: predicting the location of continuous epitopes and patterns in proteins. " Journal of Molecular Recognition, vol 16, pp 20–22, 2003.
- S. Saha and G. Raghava, "BcePred: Prediction of continuous B-cell epitopes in antigenic sequences using physico-chemical properties. " International Conference on Artificial Immune System 2004, vol 3239, pp 197–204, 2004.
- M. J. Blythe and D. R. Flower, "Benchmarking B cellepitope prediction" Protein Science vol 14, pp 246-248, 2005.
- J. E. P. Larson, O. Lund and M. Neilsen, "Improved Method for predicting linear B-cell epitopes" Immunome Research. 2:2, 2006
- S. Saha and G. Raghava, "Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. " Proteins, vol 65: pp 40-48, 2006.
- J. Sollner and B. Mayer, "Machine learning approaches for prediction of linear B-cell epitopes on proteins". Journal of Molecular Recognition. , vol 19, pp 200-208, 2006.
- J. Chen, H. Liu,J. Yang and K. Chou, "Prediction of linear B-cell epitopes using amino acid pair antigenicity scale"Amino Acids, vol 33, pp 423-428,2007.
- S. Saha and G. Raghava,"Bcipep: A database of B-cell epitopes", BMC Genomics, Vol 6, pp 79, 2005.
- L. Wang, J. Liu, S. Zhu and Y. Y. Gao, "Prediction of Linear B-cell epitopes using AAT scale" Third International Conference on Bioinformatics and Biomedical Engineering, ICBBE, pp 1-4, 2009.
- Y. EL-Manzalawy, D. Dobbs and V. Honavar, "Predicting linear B-cell epitopes using string kernels". J. Mol. Recognit. , vol 21, pp 243-255, 2008.
- Y. EL-Manzalawy, D. Dobbs and V. Honavar, "Predicting flexible length linear Bcellepitopes"7th International Conference on Computational Systems Bioinformatics, pp 121-131, 2008.
- W. Zhang and Y. Niu,"Predicting flexible length linear B-cell epitopes using pair wise sequence similarity", Third International Conference on Biomedical engineering and Informatics, 2010.
- L. JK. Wee, D. Simarmata,,Y. Kam, F P. Lisa and J. C. Tong "SVM-based prediction of linear B-cell epitopes using Bayes Feature Extraction" BMC Genomics, vol 11,Dec 2010.
- H. W. Wang,Y. C. Lin and H. T. Chang," Prediction of B-cell linear epitopes with a combination of support vector machine classification and amino acid propensity identification"Journal of Biomedicine and Biotechnology, June 2011.
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