An Introduction to B-Cell Epitope Mapping and In Silico Epitope Prediction

Abstract

Identification of B-cell epitopes is a fundamental step for development of epitope-based vaccines, therapeutic antibodies, and diagnostic tools. Epitope-based antibodies are currently the most promising class of biopharmaceuticals. In the last decade, in-depth in silico analysis and categorization of the experimentally identified epitopes stimulated development of algorithms for epitope prediction. Recently, various in silico tools are employed in attempts to predict B-cell epitopes based on sequence and/or structural data. The main objective of epitope identification is to replace an antigen in the immunization, antibody production, and serodiagnosis. The accurate identification of B-cell epitopes still presents major challenges for immunologists. Advances in B-cell epitope mapping and computational prediction have yielded molecular insights into the process of biorecognition and formation of antigen-antibody complex, which may help to localize B-cell epitopes more precisely. In this paper, we have comprehensively reviewed state-of-the-art experimental methods for B-cell epitope identification, existing databases for epitopes, and novel in silico resources and prediction tools available online. We have also elaborated new trends in the antibody-based epitope prediction. The aim of this review is to assist researchers in identification of B-cell epitopes.

Identification of a Novel Linear B-Cell Epitope on the Nucleocapsid Protein of Porcine Deltacoronavirus

“…Structural methods include X-ray crystallography, which can precisely locate the epitope position but it is limited to small soluble proteins, the method is also time consuming and costly, together these impede its widespread use [37]. Functional methods are used to detect the binding activity of antibody with antigen fragments, synthetic peptides or recombinant antigens, and have the advantage of being simpler to conduct [37]. Here, the epitope region recognized by 4E88 (308-AKPKQQKKPKK-318 aa) was determined by serially truncating the N3 portion of the N-protein.…”

Cloning, Sequencing and In Silico Characterization of OmpF Protein of Salmonella typhimurium for its Immune-Potential

“…Based on primary structure, physiochemical properties of OmpF protein was also deduced using ExPASy ProtParam (Gasteiger et al, 2005). The B cell epitopes of OmpF protein was identified and characterized using BepiPred prediction tool of IEDB analysis (Potocnakova et al, 2016). The sequence was loaded into the tool window and searched for most potential linear epitopes.…”

Identification of B‐ and T‐cell epitopes on HtrA protein of Orientia tsutsugamushi

“…45 In the I-TASSER generated model, the C-score was −0.69, estimated TM-score was 0.63 ± 0.14. The functional B-cell epitopes span 15 to 25 residues with surface accessibility for efficient antigen-antibody interactions.…”