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T-Cell Epitope Prediction Methods: An Overview

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Immunoinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1184))

Abstract

The scientific community is overwhelmed by the voluminous increase in the quantum of data on biological systems, including but not limited to the immune system. Consequently, immunoinformatics databases are continually being developed to accommodate this ever increasing data and analytical tools are continually being developed to analyze the same. Therefore, researchers are now equipped with numerous databases, analytical and prediction tools, in anticipation of better means of prevention of and therapeutic intervention in diseases of humans and other animals.

Epitope is a part of an antigen, recognized either by B- or T-cells and/or molecules of the host immune system. Since only a few amino acid residues that comprise an epitope (instead of the whole protein) are sufficient to elicit an immune response, attempts are being made to identify or predict this critical stretch or patch of amino acid residues, i.e., T-cell epitopes and B-cell epitopes to be included in multiple-subunit vaccines.

T-cell epitope prediction is a challenge owing to the high degree of MHC polymorphism and disparity in the volume of data on various steps encountered in the generation and presentation of T-cell epitopes in the living systems. Many algorithms/methods developed to predict T-cell epitopes and Web servers incorporating the same are available. These are based on approaches like considering amphipathicity profiles of proteins, sequence motifs, quantitative matrices (QM), artificial neural networks (ANN), support vector machines (SVM), quantitative structure activity relationship (QSAR) and molecular docking simulations, etc. This chapter aims to introduce the reader to the principle(s) underlying some of these methods/algorithms as well as procedural and practical aspects of using the same.

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Acknowledgements

D.V.D. and U.K.K. gratefully acknowledge financial support under the aegis of Center of Excellence (CoE) grant from the Department of Biotechnology (DBT), Government of India.

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Authors and Affiliations

  1. Bioinformatics Centre, University of Pune, Ganeshkhind Road, Pune, Maharashtra, 411007, India

    Dattatraya V. Desai & Urmila Kulkarni-Kale

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  1. Dattatraya V. Desai
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  2. Urmila Kulkarni-Kale
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Correspondence to Urmila Kulkarni-Kale .

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Editors and Affiliations

  1. Indian Statistical Institute, Kolkata, West Bengal, India

    Rajat K. De

  2. Indian Statistical Institute, Kolkata, West Bengal, India

    Namrata Tomar

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Desai, D.V., Kulkarni-Kale, U. (2014). T-Cell Epitope Prediction Methods: An Overview. In: De, R., Tomar, N. (eds) Immunoinformatics. Methods in Molecular Biology, vol 1184. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1115-8_19

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  • DOI: https://doi.org/10.1007/978-1-4939-1115-8_19

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1114-1

  • Online ISBN: 978-1-4939-1115-8

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