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In Silico Prediction of Linear B-Cell Epitopes on Proteins

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Prediction of Protein Secondary Structure

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1484))

Abstract

Antibody-protein interactions play a critical role in the humoral immune response. B-cells secrete antibodies, which bind antigens (e.g., cell surface proteins of pathogens). The specific parts of antigens that are recognized by antibodies are called B-cell epitopes. These epitopes can be linear, corresponding to a contiguous amino acid sequence fragment of an antigen, or conformational, in which residues critical for recognition may not be contiguous in the primary sequence, but are in close proximity within the folded protein 3D structure.

Identification of B-cell epitopes in target antigens is one of the key steps in epitope-driven subunit vaccine design, immunodiagnostic tests, and antibody production. In silico bioinformatics techniques offer a promising and cost-effective approach for identifying potential B-cell epitopes in a target vaccine candidate. In this chapter, we show how to utilize online B-cell epitope prediction tools to identify linear B-cell epitopes from the primary amino acid sequence of proteins.

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Acknowledgments

This work was supported by NIH grant GM066387 to VGH and DD, by Edward Frymoyer Chair of Information Sciences and Technology at Pennsylvania State University to VGH, and by a Presidential Initiative for Interdisciplinary Research (PIIR) award from Iowa State University to DD.

Author information

Authors and Affiliations

  1. College of Information Sciences and Technology, Pennsylvania State University, 301A Information Sciences and Technology Building, University Park, PA, 16802, USA

    Yasser EL-Manzalawy & Vasant G. Honavar

  2. Genetics, Development and Cell Biology Department, Iowa State University, Ames, IA, 50011, USA

    Drena Dobbs

Authors
  1. Yasser EL-Manzalawy
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  2. Drena Dobbs
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  3. Vasant G. Honavar
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Corresponding author

Correspondence to Vasant G. Honavar .

Editor information

Editors and Affiliations

  1. Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, Queensland, Australia

    Yaoqi Zhou

  2. Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA

    Andrzej Kloczkowski

  3. Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA

    Eshel Faraggi

  4. Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, Queensland, Australia

    Yuedong Yang

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EL-Manzalawy, Y., Dobbs, D., Honavar, V.G. (2017). In Silico Prediction of Linear B-Cell Epitopes on Proteins. In: Zhou, Y., Kloczkowski, A., Faraggi, E., Yang, Y. (eds) Prediction of Protein Secondary Structure. Methods in Molecular Biology, vol 1484. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6406-2_17

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  • DOI: https://doi.org/10.1007/978-1-4939-6406-2_17

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6404-8

  • Online ISBN: 978-1-4939-6406-2

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