Abstract
Linear B-cell epitope prediction research has received a steadily growing interest ever since the first method was developed in 1981. B-cell epitope identification with the help of an accurate prediction method can lead to an overall faster and cheaper vaccine design process, a crucial necessity in the COVID-19 era. Consequently, several B-cell epitope prediction methods have been developed over the past few decades, but without significant success. In this study, we review the current performance and methodology of some of the most widely used linear B-cell epitope predictors which are available via a command-line interface, namely, BcePred, BepiPred, ABCpred, COBEpro, SVMTriP, LBtope, and LBEEP. Additionally, we attempted to remedy performance issues of the individual methods by developing a consensus classifier, which combines the separate predictions of these methods into a single output, accelerating the epitope-based vaccine design. While the method comparison was performed with some necessary caveats and individual methods might perform much better for specialized datasets, we hope that this update in performance can aid researchers towards the choice of a predictor, for the development of biomedical applications such as designed vaccines, diagnostic kits, immunotherapeutics, immunodiagnostic tests, antibody production, and disease diagnosis and therapy.
Highlights
B-cell epitopes are regions on the surface of an antigen, to which specific antibodies recognize and bind, triggering the immune response [1]
B-cell epitopes are divided into two categories: linear epitopes, which consist of a linear sequence of residues; and conformational epitopes, which consist of residues that are not contiguous in the primary protein sequence but are brought together by the folded protein structure [10]
The second criterion was that methods should be usable via a Command-Line Interface (CLI) and through a Graphical User Interface (GUI) and the third criterion was that each method’s way of operation should be somewhat comparable and in tune with the rest of the available predictors
Summary
B-cell epitopes are regions on the surface of an antigen, to which specific antibodies recognize and bind, triggering the immune response [1]. The ability to identify these binding areas in the antigen’s sequence or structure is important for the development of synthetic vaccines [3,4,5], diagnostic tests [6], and immunotherapeutics [7,8], especially in the COVID-19 era Focus on these applications through the lens of epitope discovery has gained attention over the years, especially in regard to the safety benefits of synthetic vaccine development [9]. The vast majority of B-cell epitopes have been estimated to be conformational, while only a fraction are linear [11]
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