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Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis

Yan Xin Huang12, Yong Li Bao3*, Shu Yan Guo3, Yan Wang2, Chun Guang Zhou2 and Yu Xin Li14*

Author Affiliations

1 Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, PR China

2 College of Computer Science and Technology, Jilin University, Changchun 130012, PR China

3 Research Center of Agriculture and Medicine Gene Engineering of Ministry of Education, Northeast Normal University, Changchun 130024, PR China

4 National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun 130024, PR China

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BMC Bioinformatics 2008, 9:538  doi:10.1186/1471-2105-9-538

Published: 16 December 2008



The prediction of conformational B-cell epitopes is one of the most important goals in immunoinformatics. The solution to this problem, even if approximate, would help in designing experiments to precisely map the residues of interaction between an antigen and an antibody. Consequently, this area of research has received considerable attention from immunologists, structural biologists and computational biologists. Phage-displayed random peptide libraries are powerful tools used to obtain mimotopes that are selected by binding to a given monoclonal antibody (mAb) in a similar way to the native epitope. These mimotopes can be considered as functional epitope mimics. Mimotope analysis based methods can predict not only linear but also conformational epitopes and this has been the focus of much research in recent years. Though some algorithms based on mimotope analysis have been proposed, the precise localization of the interaction site mimicked by the mimotopes is still a challenging task.


In this study, we propose a method for B-cell epitope prediction based on mimotope analysis called Pep-3D-Search. Given the 3D structure of an antigen and a set of mimotopes (or a motif sequence derived from the set of mimotopes), Pep-3D-Search can be used in two modes: mimotope or motif. To evaluate the performance of Pep-3D-Search to predict epitopes from a set of mimotopes, 10 epitopes defined by crystallography were compared with the predicted results from a Pep-3D-Search: the average Matthews correlation oefficient (MCC), sensitivity and precision were 0.1758, 0.3642 and 0.6948. Compared with other available prediction algorithms, Pep-3D-Search showed comparable MCC, specificity and precision, and could provide novel, rational results. To verify the capability of Pep-3D-Search to align a motif sequence to a 3D structure for predicting epitopes, 6 test cases were used. The predictive performance of Pep-3D-Search was demonstrated to be superior to that of other similar programs. Furthermore, a set of test cases with different lengths of sequences was constructed to examine Pep-3D-Search's capability in searching sequences on a 3D structure. The experimental results demonstrated the excellent search capability of Pep-3D-Search, especially when the length of the query sequence becomes longer; the iteration numbers of Pep-3D-Search to precisely localize the target paths did not obviously increase. This means that Pep-3D-Search has the potential to quickly localize the epitope regions mimicked by longer mimotopes.


Our Pep-3D-Search provides a powerful approach for localizing the surface region mimicked by the mimotopes. As a publicly available tool, Pep-3D-Search can be utilized and conveniently evaluated, and it can also be used to complement other existing tools. The data sets and open source code used to obtain the results in this paper are available on-line and as supplementary material. More detailed materials may be accessed at webcite.