Conformational B-Cell Epitopes Prediction from Sequences Using Cost-Sensitive Ensemble Classifiers and Spatial Clustering
Joint Authors
Zhao, Xiaowei
Zhang, Jian
Gao, Bo
Sun, Pingping
Ma, Zhiqiang
Source
Issue
Vol. 2014, Issue 2014 (31 Dec. 2014), pp.1-12, 12 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2014-06-17
Country of Publication
Egypt
No. of Pages
12
Main Subjects
Abstract EN
B-cell epitopes are regions of the antigen surface which can be recognized by certain antibodies and elicit the immune response.
Identification of epitopes for a given antigen chain finds vital applications in vaccine and drug research.
Experimental prediction of B-cell epitopes is time-consuming and resource intensive, which may benefit from the computational approaches to identify B-cell epitopes.
In this paper, a novel cost-sensitive ensemble algorithm is proposed for predicting the antigenic determinant residues and then a spatial clustering algorithm is adopted to identify the potential epitopes.
Firstly, we explore various discriminative features from primary sequences.
Secondly, cost-sensitive ensemble scheme is introduced to deal with imbalanced learning problem.
Thirdly, we adopt spatial algorithm to tell which residues may potentially form the epitopes.
Based on the strategies mentioned above, a new predictor, called CBEP (conformational B-cell epitopes prediction), is proposed in this study.
CBEP achieves good prediction performance with the mean AUC scores (AUCs) of 0.721 and 0.703 on two benchmark datasets (bound and unbound) using the leave-one-out cross-validation (LOOCV).
When compared with previous prediction tools, CBEP produces higher sensitivity and comparable specificity values.
A web server named CBEP which implements the proposed method is available for academic use.
American Psychological Association (APA)
Zhang, Jian& Zhao, Xiaowei& Sun, Pingping& Gao, Bo& Ma, Zhiqiang. 2014. Conformational B-Cell Epitopes Prediction from Sequences Using Cost-Sensitive Ensemble Classifiers and Spatial Clustering. BioMed Research International،Vol. 2014, no. 2014, pp.1-12.
https://search.emarefa.net/detail/BIM-490707
Modern Language Association (MLA)
Zhang, Jian…[et al.]. Conformational B-Cell Epitopes Prediction from Sequences Using Cost-Sensitive Ensemble Classifiers and Spatial Clustering. BioMed Research International No. 2014 (2014), pp.1-12.
https://search.emarefa.net/detail/BIM-490707
American Medical Association (AMA)
Zhang, Jian& Zhao, Xiaowei& Sun, Pingping& Gao, Bo& Ma, Zhiqiang. Conformational B-Cell Epitopes Prediction from Sequences Using Cost-Sensitive Ensemble Classifiers and Spatial Clustering. BioMed Research International. 2014. Vol. 2014, no. 2014, pp.1-12.
https://search.emarefa.net/detail/BIM-490707
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-490707