Multi‐perspectives and challenges in identifying B‐cell epitopes

Abstract

The identification of B‐cell epitopes in antigens is a crucial step in developing recombinant vaccines or immunotherapies for various diseases. Over the past four decades, numerous in silico methods have been developed for predicting B‐cell epitopes. However, existing reviews have only covered specific aspects, such as the progress in predicting conformational or linear B‐cell epitopes. Therefore, in this paper, we have undertaken a systematic approach to provide a comprehensive review covering all aspects associated with the identification of B‐cell epitopes. Firstly, we have covered the experimental techniques developed over the years for identifying linear and conformational epitopes, including the limitations and challenges associated with these techniques. Secondly, we have briefly described the historical perspectives and resources that maintain experimentally validated information on B‐cell epitopes. Thirdly, we have extensively reviewed the computational methods developed for predicting conformational B‐cell epitopes from the structure of the antigen, as well as the methods for predicting conformational epitopes from the sequence. Fourthly, we have systematically reviewed the in silico methods developed in the last four decades for predicting linear or continuous B‐cell epitopes. Finally, we have discussed the overall challenge of identifying continuous or conformational B‐cell epitopes. In this review, we only listed major computational resources; a complete list with the URL is available from the BCinfo website (https://webs.iiitd.edu.in/raghava/bcinfo/ ).This article is protected by copyright. All rights reserved.

Utilizing Extraepitopic Amino Acid Substitutions to Define Changes in the Accessibility of Conformational Epitopes of the Bacillus cereus HlyII C-Terminal Domain

“…The identification of epitopes is important in the development of highly specific and harmless vaccines, and therapeutic and diagnostic antibodies [17,18], since epitopes, namely, allow the immune system to recognize and respond to specific pathogens [19]. Therefore, it is especially important to determine the epitope of an antibody capable of neutralizing one of the significant pathogenic factors of B. cereus in order to design a mimetic, based on which a protection against the action of HlyII of various B. cereus strains can be created.…”

Effect of food processing on the immunoreactivity of gliadin

“…Later, the silico programme was proposed to predict the antigenic epitope for both linear and conformational epitopes. However, the accurate identification of epitopes remains the major challenge for immunoinformaticians (Sun et al ., 2019; Kumar et al ., 2023). Recently, several prediction epitopes methods have been developed, and many studies reported several sites to predict linear epitopes such as BcePred, BepiPred, ABCpred, COBEpro, SVMTriP, LBtope, Emini and LBEEP (Isea, 2017; Manavalan et al ., 2018).…”

“…However, the distinction between CD and NCGS depends on patients' symptoms, according to the European Society for Paediatric Gastroenterology, Hepatology and Nutrition (Tonutti & Bizzaro, 2014; Leonard et al ., 2017). The gluten disorder related to the immune system is producing antibodies against short sequencing of amino acids called epitope (Sanchez‐Trincado et al ., 2017; Kumar et al ., 2023). Many epitopes related to gluten disorder have been identified and listed in various review papers (Panda et al ., 2017; Panda & Garber, 2019a, 2019b), which are later used to follow gluten reduction as a result of treating gluten by food processing techniques.…”