Identification of conformational B-cell Epitopes in an antigen from its primary sequenceReport as inadecuate




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Immunome Research

, 6:6

First Online: 20 October 2010Received: 20 May 2010Accepted: 20 October 2010

Abstract

BackgroundOne of the major challenges in the field of vaccine design is to predict conformational B-cell epitopes in an antigen. In the past, several methods have been developed for predicting conformational B-cell epitopes in an antigen from its tertiary structure. This is the first attempt in this area to predict conformational B-cell epitope in an antigen from its amino acid sequence.

ResultsAll Support vector machine SVM models were trained and tested on 187 non-redundant protein chains consisting of 2261 antibody interacting residues of B-cell epitopes. Models have been developed using binary profile of pattern BPP and physiochemical profile of patterns PPP and achieved a maximum MCC of 0.22 and 0.17 respectively. In this study, for the first time SVM model has been developed using composition profile of patterns CPP and achieved a maximum MCC of 0.73 with accuracy 86.59%. We compare our CPP based model with existing structure based methods and observed that our sequence based model is as good as structure based methods.

ConclusionThis study demonstrates that prediction of conformational B-cell epitope in an antigen is possible from is primary sequence. This study will be very useful in predicting conformational B-cell epitopes in antigens whose tertiary structures are not available. A web server CBTOPE has been developed for predicting B-cell epitope http:-www.imtech.res.in-raghava-cbtope-.

Electronic supplementary materialThe online version of this article doi:10.1186-1745-7580-6-6 contains supplementary material, which is available to authorized users.

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Author: Hifzur Rahman Ansari - Gajendra PS Raghava

Source: https://link.springer.com/







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