Estimation and extraction of B-cell linear epitopes predicted by mathematical morphology approaches

✍ Scribed by Hao-Teng Chang; Chih-Hong Liu; Tun-Wen Pai

• Publisher: John Wiley and Sons
• Year: 2008
• Tongue: English
• Weight: 481 KB
• Volume: 21
• Category: Article
• ISSN: 0952-3499
• DOI: 10.1002/jmr.910

✦ Synopsis

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. Copyright © 2008 John Wiley & Sons, Ltd.