title: Conformational B-cell epitopes prediction from sequences using cost-sensitive ensemble classifiers and spatial clustering.
abstract: 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.
authors.affiliation: School of Computer Science and Information Technology, Northeast Normal University, Changchun 1300117, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Zhang
authors.affiliation: School of Computer Science and Information Technology, Northeast Normal University, Changchun 1300117, China.
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Zhao
authors.affiliation: School of Computer Science and Information Technology, Northeast Normal University, Changchun 1300117, China ; The Engineering Laboratory for Drug-Gene and Protein Screening, Northeast Normal University, Changchun 1300117, China.
authors.forename: Pingping
authors.initials: P
authors.lastname: Sun
authors.affiliation: School of Computer Science and Information Technology, Northeast Normal University, Changchun 1300117, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Gao
authors.affiliation: School of Computer Science and Information Technology, Northeast Normal University, Changchun 1300117, China.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Ma
mesh_terms: D000465:Algorithms; D000941:Antigens / Q000235:genetics / Q000276:immunology; D001483:Base Sequence; D019295:Computational Biology; D003362:Cost-Benefit Analysis; D018985:Epitopes, B-Lymphocyte / Q000235:genetics / Q000276:immunology*; D006801:Humans; D007113:Immunity, Innate; D020407:Internet; D008968:Molecular Conformation; D012984:Software
chemical_list: D000941:Antigens; D018985:Epitopes, B-Lymphocyte