Prediction of B cell epitopes in proteins using a novel sequence similarity-based method

Abstract

Prediction of B cell epitopes that can replace the antigen for antibody production and detection is of great interest for research and the biotech industry. Here, we developed a novel BLAST-based method to predict linear B cell epitopes. To that end, we generated a BLAST-formatted database upon a dataset of 62,730 known linear B cell epitope sequences and considered as a B cell epitope any peptide sequence producing ungapped BLAST hits to this database with identity ≥ 80% and length ≥ 8. We examined B cell epitope predictions by this method in tenfold cross-validations in which we considered various types of non-B cell epitopes, including 62,730 peptide sequences with verified negative B cell assays. As a result, we obtained values of accuracy, specificity and sensitivity of 72.54 ± 0.27%, 81.59 ± 0.37% and 63.49 ± 0.43%, respectively. In an independent dataset incorporating 503 B cell epitopes, this method reached accuracy, specificity and sensitivity of 74.85%, 99.20% and 50.50%, respectively, outperforming state-of-the-art methods to predict linear B cell epitopes. We implemented this BLAST-based approach to predict B cell epitopes at http://imath.med.ucm.es/bepiblast.

An Immunoinformatic‐Based In Silico Identification on the Creation of a Multiepitope‐Based Vaccination Against the Nipah Virus

“…The selected B cell epitope is then subjected to tests for toxicity (ToxinPred), allergenicity (AllerTOP v2.0), and antigenicity (VaxiJen v2.0). The ungapped epitopes, minimum identity, and peptide length proteins used to identify B cell epitopes can be modified easily by the user for further predictions and constructions of vaccine candidates [ 67 ]. The 10 B cell epitopes were found suitable after passing the selection criteria out of 34 B cell epitopes (lengths ranging from 8 to 50).…”

Tendências Biotecnológicas Sustentáveis para Fins de Saúde Única

“…A predição de epítopos pra linfócitos B tem busca identificar estruturas que levam à produção de anticorpos (Ras-Carmona et al, 2022). Os epítopos conformacionais são estruturalmente mais complexos, formados por regiões não sequenciais e geralmente em estruturas tridimensionais (Cia;Pucci;Rooman, 2023).…”

Recent Progress in Antibody Epitope Prediction

“…Any peptide can be considered a B cell epitope if producing ungapped BLAST hits this database with an identity ≥ 80% and length ≥ 8. Interestingly, the BLAST-based approach obtained values for the accuracy, specificity, and sensitivity of 72.54 ± 0.27%, 81.59 ± 0.37%, and 63.49 ± 0.43%, respectively [ 52 ].…”