Fundamentals and Methods for T- and B-Cell Epitope Prediction

Abstract

Adaptive immunity is mediated by T- and B-cells, which are immune cells capable of developing pathogen-specific memory that confers immunological protection. Memory and effector functions of B- and T-cells are predicated on the recognition through specialized receptors of specific targets (antigens) in pathogens. More specifically, B- and T-cells recognize portions within their cognate antigens known as epitopes. There is great interest in identifying epitopes in antigens for a number of practical reasons, including understanding disease etiology, immune monitoring, developing diagnosis assays, and designing epitope-based vaccines. Epitope identification is costly and time-consuming as it requires experimental screening of large arrays of potential epitope candidates. Fortunately, researchers have developed in silico prediction methods that dramatically reduce the burden associated with epitope mapping by decreasing the list of potential epitope candidates for experimental testing. Here, we analyze aspects of antigen recognition by T- and B-cells that are relevant for epitope prediction. Subsequently, we provide a systematic and inclusive review of the most relevant B- and T-cell epitope prediction methods and tools, paying particular attention to their foundations.

Identification and characterization of protective CD8+ T‐epitopes in a malaria vaccine candidate SLTRiP

“…We, therefore, synthesized multiple fragments of our gene to identify protective regions. The in silico studies have shown that the epitopes for T‐cells are generally present in hydrophobic regions of protein while hydrophilic regions score best for B‐cell epitopes . Using this information, bioinformatics approach was employed to identify hydrophobic regions of the protein using Parker hydrophilicity prediction to identify hydrophobic regions in protein.…”

“…25 Epitope mapping has multiple advantages for vaccine development as they represent antigenic regions of the protein and consequently nonprotective parts can be removed. 26,27 Epitopes from different alleles can also be collected for the formation of a peptide library that will be recognized by majority of immune populations. In addition, using mouse model, the peptide-specific protective efficacy can be characterized by mice immunization.…”

“…The in silico studies have shown that the epitopes for T-cells are generally present in hydrophobic regions of protein while hydrophilic regions score best for B-cell epitopes. 27 Using this information, bioinformatics approach was employed to identify hydrophobic regions of the protein using Parker hydrophilicity prediction to identify hydrophobic regions in protein. By generating recombinant subfragments of the protein SLTRiP, we observed that the immunodominant T-cell epitopes of the protein are located between amino acids 155 and 355, which forms the protective SLTRiP C3 and SLTRiP C4 fragments of protein SLTRiP.…”

In Silico Identification and in Vitro Analysis of B and T-Cell Epitopes of the Black Turtle Bean (Phaseolus Vulgaris L.) Lectin

“…With an enormous expansion in knowledge and data about 3-D structures and epitopes of identified allergens, a large number of computational algorithms were developed [17,33,34]. The online tools are fast, precise and extremely efficient means of structure identification and mapping of epitope regions [35,36]. Since the prediction accuracy of combined methods for B and T-cell epitope prediction is far higher than any single in silico tool, consensus method was used as it combined the strengths of different prediction algorithms [19,35].…”

<p>Immunoinformatics and Vaccine Development: An Overview</p>

“…138 Now, antibody-binding sites in a given HLA (MHC) molecule are mostly prediction-servers predetermined on the basis of particular binding motifs and the anchor residues. 139,140 These residues refer to known amino acids located at defined locations in the peptide chain and which are peculiar to each MHC molecule. 141,142 Prediction-server database of peptide motifs and/or of MHC ligands may be obtained from web-based and/or from prediction-servers dedicated to NetMHC family.…”