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. 2013 May 7;8(5):e62216.
doi: 10.1371/journal.pone.0062216. Print 2013.

Improved method for linear B-cell epitope prediction using antigen's primary sequence

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Improved method for linear B-cell epitope prediction using antigen's primary sequence

Harinder Singh et al. PLoS One. .

Abstract

One of the major challenges in designing a peptide-based vaccine is the identification of antigenic regions in an antigen that can stimulate B-cell's response, also called B-cell epitopes. In the past, several methods have been developed for the prediction of conformational and linear (or continuous) B-cell epitopes. However, the existing methods for predicting linear B-cell epitopes are far from perfection. In this study, an attempt has been made to develop an improved method for predicting linear B-cell epitopes. We have retrieved experimentally validated B-cell epitopes as well as non B-cell epitopes from Immune Epitope Database and derived two types of datasets called Lbtope_Variable and Lbtope_Fixed length datasets. The Lbtope_Variable dataset contains 14876 B-cell epitope and 23321 non-epitopes of variable length where as Lbtope_Fixed length dataset contains 12063 B-cell epitopes and 20589 non-epitopes of fixed length. We also evaluated the performance of models on above datasets after removing highly identical peptides from the datasets. In addition, we have derived third dataset Lbtope_Confirm having 1042 epitopes and 1795 non-epitopes where each epitope or non-epitope has been experimentally validated in at least two studies. A number of models have been developed to discriminate epitopes and non-epitopes using different machine-learning techniques like Support Vector Machine, and K-Nearest Neighbor. We achieved accuracy from ∼54% to 86% using diverse s features like binary profile, dipeptide composition, AAP (amino acid pair) profile. In this study, for the first time experimentally validated non B-cell epitopes have been used for developing method for predicting linear B-cell epitopes. In previous studies, random peptides have been used as non B-cell epitopes. In order to provide service to scientific community, a web server LBtope has been developed for predicting and designing B-cell epitopes (http://crdd.osdd.net/raghava/lbtope/).

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Conflict of interest statement

Competing Interests: Dr. G.P.S Raghava is a member of PLOS ONE Editorial Board. This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials.

Figures

Figure 1
Figure 1. Length-wise distribution of peptides (B-cell epitopes and non-epitopes), we divided peptides in different bins like peptides having a length less than five residues, having residues between 5 to 10 residues.
Figure 2
Figure 2. Two-sample logo showing dominance of surface accessible residues in B-cell epitopes.
Yellow and black color residues indicate to surface accessible and non-accessible residues respectively.

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References

    1. Tomar N, De RK (2010) Immunoinformatics: an integrated scenario. Immunology 131: 153–168. - PMC - PubMed
    1. Dudek NL, Perlmutter P, Aguilar MI, Croft NP, Purcell AW (2010) Epitope discovery and their use in peptide based vaccines. Curr Pharm Des 16: 3149–3157. - PubMed
    1. Bryson CJ, Jones TD, Baker MP (2010) Prediction of immunogenicity of therapeutic proteins: validity of computational tools. BioDrugs 24: 1–8. - PubMed
    1. Steere AC, Drouin EE, Glickstein LJ (2011) Relationship between immunity to Borrelia burgdorferi outer-surface protein A (OspA) and Lyme arthritis. Clin Infect Dis 52 Suppl 3s259–265. - PMC - PubMed
    1. El-Manzalawy Y, Honavar V (2010) Recent advances in B-cell epitope prediction methods. Immunome Res 6 Suppl 2S2. - PMC - PubMed

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Grants and funding

The authors are thankful to the Council of Scientific and Industrial Research (CSIR) and Department of Biotechnology (DBT), Government of India for financial assistance is duly acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.