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EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results

DOI: 10.1186/1471-2105-11-381

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In this work, we present two novel server applications for discontinuous epitope prediction: EPSVR and EPMeta, where EPMeta is a meta server. EPSVR, EPMeta, and datasets are available at http://sysbio.unl.edu/services webcite.The server application for discontinuous epitope prediction, EPSVR, uses a Support Vector Regression (SVR) method to integrate six scoring terms. Furthermore, we combined EPSVR with five existing epitope prediction servers to construct EPMeta. All methods were benchmarked by our curated independent test set, in which all antigens had no complex structures with the antibody, and their epitopes were identified by various biochemical experiments. The area under the receiver operating characteristic curve (AUC) of EPSVR was 0.597, higher than that of any other existing single server, and EPMeta had a better performance than any single server - with an AUC of 0.638, significantly higher than PEPITO and Disctope (p-value < 0.05).Antigenic epitopes are regions of protein surface that are preferentially recognized by antibodies. Prediction of antigenic epitopes can help during the design of vaccine components and immuno-diagnostic reagents, but predicting effective epitopes is still an open problem in bioinformatics. Usually, B-cell antigenic epitopes are classified as either continuous or discontinuous. The majority of available epitope prediction methods focus on continuous epitopes [1-12].Although discontinuous epitopes dominate most antigenic epitope families [13], due to their computational complexity, only a very limited number of prediction methods exist for discontinuous epitope prediction: CEP [14], DiscoTope [15], PEPITO [16], ElliPro [17], SEPPA [18], EPITOPIA[19,20] and our previous work, EPCES [21]. All discontinuous epitope prediction methods require the three-dimensional structure of the antigenic protein. The small number of available antigen-antibody complex structures limits the development of reliable discontinuous epitope prediction

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