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Identification of B-cell epitopes in an antigen for inducing specific class of antibodies

Sudheer Gupta1, Hifzur Rahman Ansari1, Ankur Gautam1, Open Source Drug Discovery Consortium2 and Gajendra PS Raghava1*

Author Affiliations

1 Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh 160036, India

2 Open Source Drug Discovery Unit, Council of Scientific and Industrial Research (CSIR) Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India

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Biology Direct 2013, 8:27  doi:10.1186/1745-6150-8-27

Published: 30 October 2013



In the past, numerous methods have been developed for predicting antigenic regions or B-cell epitopes that can induce B-cell response. To the best of authors’ knowledge, no method has been developed for predicting B-cell epitopes that can induce a specific class of antibody (e.g., IgA, IgG) except allergenic epitopes (IgE). In this study, an attempt has been made to understand the relation between primary sequence of epitopes and the class of antibodies generated.


The dataset used in this study has been derived from Immune Epitope Database and consists of 14725 B-cell epitopes that include 11981 IgG, 2341 IgE, 403 IgA specific epitopes and 22835 non-B-cell epitopes. In order to understand the preference of residues or motifs in these epitopes, we computed and compared amino acid and dipeptide composition of IgG, IgE, IgA inducing epitopes and non-B-cell epitopes. Differences in composition profiles of different classes of epitopes were observed, and few residues were found to be preferred. Based on these observations, we developed models for predicting antibody class-specific B-cell epitopes using various features like amino acid composition, dipeptide composition, and binary profiles. Among these, dipeptide composition-based support vector machine model achieved maximum Matthews correlation coefficient of 0.44, 0.70 and 0.45 for IgG, IgE and IgA specific epitopes respectively. All models were developed on experimentally validated non-redundant dataset and evaluated using five-fold cross validation. In addition, the performance of dipeptide-based model was also evaluated on independent dataset.


Present study utilizes the amino acid sequence information for predicting the tendencies of antigens to induce different classes of antibodies. For the first time, in silico models have been developed for predicting B-cell epitopes, which can induce specific class of antibodies. A web service called IgPred has been developed to serve the scientific community. This server will be useful for researchers working in the field of subunit/epitope/peptide-based vaccines and immunotherapy ( webcite).


This article was reviewed by Dr. M Michael Gromiha, Dr Christopher Langmead (nominated by Dr Robert Murphy) and Dr Lina Ma (nominated by Dr Zhang Zhang).

Support vector machine; Prediction; Antibody; Class-specific; B-cell epitope; Isotype