In Silico Prediction of Linear B-Cell Epitopes on Proteins

  • Yasser EL-Manzalawy
  • Drena Dobbs
  • Vasant G. Honavar
Part of the Methods in Molecular Biology book series (MIMB, volume 1484)


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.

Key words

Antibody-protein interaction B-cell epitope prediction Linear B-cell epitope prediction Epitope mapping Epitope prediction 



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.


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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Yasser EL-Manzalawy
    • 1
  • Drena Dobbs
    • 2
  • Vasant G. Honavar
    • 1
  1. 1.College of Information Sciences and TechnologyPennsylvania State UniversityUniversity ParkUSA
  2. 2.Genetics, Development and Cell Biology DepartmentIowa State UniversityAmesUSA

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