ArticlePloS one2013
Improved method for linear B-cell epitope prediction using antigen's primary sequence.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 178 papers.
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178 citing papers in PubMed.
- Design and in silico evaluation of PV-GNProtecta: an mRNA multi-epitope vaccine candidate against Puumala virus using immunoinformatics and structural analysis.Genomics & informatics · 2026Article
- Proteome-wide characterization of Plasmodium vivax antigens using a high-density peptide array.PLoS pathogens · 2026Article
- Broad-Spectrum Multi-Epitope Design Targeting Conserved Hantavirus Glycoproteins (Gn/Gc): Chimeric Antigen Engineering and Structural Mapping.International journal of molecular sciences · 2026Article
- "Just the Best Ones" combination: a new strategy for multi-epitope vaccine candidate based on immunoinformatics analysis to induce protective immunity against MRSA infection.Microbiology spectrum · 2026Article
- The critical role of artificial intelligence and bioinformatics in accelerating peptide-based vaccine discovery for tackling global infectious diseases.Briefings in bioinformatics · 2026Review
- In Silico Design and Computational Characterization of Novel Chimeric Multiepitope Antigens for Mpox Serosurveillance: An Immunoinformatics Approach.Health science reports · 2026Article
- Design of a global population-covering multi-epitope mRNA vaccine against Lassa virus using immunoinformatics.Scientific reports · 2026Article
- Design and immunogenicity of a recombinant Saccharomyces boulardii secreting the P2-VP8 subunit rotavirus vaccine.Scientific reports · 2026Article
- B-cell epitope prediction in the age of machine learning: advancements and challenges.Journal of translational medicine · 2026Review
- IFNg_DeepKG: A Novel Model for Identifying Interferon-Gamma-Inducing Epitopes Using Knowledge Graph RAG in Biomedical Applications.Journal of chemical information and modeling · 2026Article
- Article
- Immunoinformatics-driven design of a conserved RNA-dependent RNA polymerase-based multi-epitope vaccine against avian infectious bronchitis virus.Veterinary world · 2026Article
- Improving B-cell Linear Epitope PredictionCurrent drug targets · 2026Article
- The impact of biologically relevant negative samples on machine learning-based B-cell epitope prediction for Influenza A.Bioinformatics advances · 2026Article
- Article
- Systems Vaccinology-Integrated Proteomics to Develop a Novel Prophylactic and Therapeutic Vaccine Against Human Papillomavirus 16.Bioinformatics and biology insights · 2026Article
- In silico design and characterization of a novel multi-epitope mRNA vaccine candidate against Streptococcus pneumoniae.Scientific reports · 2025Article
- B cell-reactive neoantigens boost antitumor immunity.Science advances · 2025Article
- OmpA virulence factor, a promising conserved vaccine candidate against Acinetobacter baumannii, could trigger autoreactive immune responses in susceptible population.BMC immunology · 2025Article
- Computational Methods in Immunoinformatics: Epitope Discovery and Diagnostic Applications.ACS omega · 2025Review
118 more citing papers are in PubMed but not listed here.
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
One of the major challenges in designing a peptide-based vaccine is the identification of antigenic regions in an antigen that can stimulate B-cell's response, also called B-cell epitopes. In the past, several methods have been developed for the prediction of conformational and linear (or continuous) B-cell epitopes. However, the existing methods for predicting linear B-cell epitopes are far from perfection. In this study, an attempt has been made to develop an improved method for predicting linear B-cell epitopes. We have retrieved experimentally validated B-cell epitopes as well as non B-cell epitopes from Immune Epitope Database and derived two types of datasets called Lbtope_Variable and Lbtope_Fixed length datasets. The Lbtope_Variable dataset contains 14876 B-cell epitope and 23321 non-epitopes of variable length where as Lbtope_Fixed length dataset contains 12063 B-cell epitopes and 20589 non-epitopes of fixed length. We also evaluated the performance of models on above datasets after removing highly identical peptides from the datasets. In addition, we have derived third dataset Lbtope_Confirm having 1042 epitopes and 1795 non-epitopes where each epitope or non-epitope has been experimentally validated in at least two studies. A number of models have been developed to discriminate epitopes and non-epitopes using different machine-learning techniques like Support Vector Machine, and K-Nearest Neighbor. We achieved accuracy from ∼54% to 86% using diverse s features like binary profile, dipeptide composition, AAP (amino acid pair) profile. In this study, for the first time experimentally validated non B-cell epitopes have been used for developing method for predicting linear B-cell epitopes. In previous studies, random peptides have been used as non B-cell epitopes. In order to provide service to scientific community, a web server LBtope has been developed for predicting and designing B-cell epitopes (http://crdd.osdd.net/raghava/lbtope/).
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