title: Estimation and extraction of B-cell linear epitopes predicted by mathematical morphology approaches.
abstract: B-cell epitope prediction facilitates the design and synthesis of short peptides for various immunological applications. Several algorithms have been developed to predict B-cell linear epitopes (LEs) from primary sequences of antigens, providing important information for immunobiological experiments and antibody design. This paper describes two robust methods, LE prediction with/without local peak extraction (LEP-LP and LEP-NLP), based on antigenicity scale and mathematical morphology for the prediction of B-cell LEs. Previous studies revealed that LEs could occur in regions with low-to-moderate but not globally high antigenicity scales. Hence, we developed a method adopting mathematical morphology to extract local peaks from a linear combination of the propensity scales of physico-chemical characteristics at each antigen residue. Comparison among LEP-LP/LEP-NLP, BepiPred and BEPITOPE revealed that our algorithms performed better in retrieving epitopes with low-to-moderate antigenicity and achieved comparable performance according to receiver operation characteristics (ROC) curve analysis. Of the identified LEs, over 30% were unable to be predicted by BepiPred and BEPITOPE employing an average threshold of antigenicity index or default settings. Our LEP-LP method provides a bioinformatics approach for predicting B-cell LEs with low- to-moderate antigenicity. The web-based server was established at http://biotools.cs.ntou.edu.tw/lepd_antigenicity. php for free use.
authors.affiliation: Graduate Institute of Molecular Systems Biomedicine, China Medical University, Taichung, Taiwan, ROC.
authors.forename: Hao-Teng
authors.initials: HT
authors.lastname: Chang
authors.forename: Chih-Hong
authors.initials: CH
authors.lastname: Liu
authors.forename: Tun-Wen
authors.initials: TW
authors.lastname: Pai
mesh_terms: D000465:Algorithms; D000941:Antigens / Q000276:immunology; D019295:Computational Biology / Q000379:methods; D018985:Epitopes, B-Lymphocyte / Q000032:analysis* / Q000276:immunology*; D020407:Internet; D008433:Mathematics
chemical_list: D000941:Antigens; D018985:Epitopes, B-Lymphocyte