ArticleProtein science : a publication of the Protein Society2022
BepiPred-3.0: Improved B-cell epitope prediction using protein language models.
Article in Protein science : a publication of the Protein Society, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 177 papers, 2 of them syntheses that pooled it.
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Who cites it
177 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- An integrated AI-driven vaccine design process: a systematic review of workflows from generative design to translational prediction.Immunologic research · 2026Pooled it
- Opportunities and challenges with artificial intelligence in allergy and immunology: a bibliometric study.Frontiers in medicine · 2025Pooled it
- A bivalent subunit bovine herpesvirus 1 vaccine based on the ectodomains of glycoproteins D and B elicits robust protective immunity against infection in a rabbit model.The veterinary quarterly · 2026Article
- Computational design and translational development of TCR-mimic scFv antibodies for peptide-HLA neoantigen targeting.npj drug discovery · 2026Review
- Targeting Amastigote and Trypomastigote Phases: Multi-Epitope Vaccine Strategy Against Trypanosoma cruzi.Biotechnology and applied biochemistry · 2026Article
- Computational identification of conserved B- and T-cell epitopes for multi-epitope peptide vaccine design against bovine leukemia virus.Virus genes · 2026Article
- Evolutionary Dynamics-AwareACS omega · 2026Article
- Comparative Genomics-Guided Epitope Prioritization and in Silico Design of a Multi-Epitope DNA Vaccine Candidate Against Megalocytivirus pagrus 1.Marine biotechnology (New York, N.Y.) · 2026Article
- Integrated immunoinformatics for the design of novel multi-epitope vaccine and identification of new drug targets against Stenotrophomonas maltophilia, a multidrug-resistant superbug.Journal, genetic engineering & biotechnology · 2026Article
- Surf2Spot: a surface-informed geometry-aware model for predicting partner-independent binder and nanobody design hotspots.Briefings in bioinformatics · 2026Article
- PatchEpi: patch-aware equivariant learning improves structure-based epitope prediction.Bioinformatics (Oxford, England) · 2026Article
- In silico pharmacological evaluation of a multi-epitope vaccine candidate targeting the G1 and G2 glycoproteins of Oropouche virus via TLR3 interaction.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Isolation and Genomic Characteristics of the First Bovine Viral Diarrhea Virus Subgenotype 2b Isolate from Buffalo in Guangxi Province, China.Microorganisms · 2026Article
- Structure-Guided Immunoinformatics for the Rational Design of a Multi-Epitope Vaccine Against Batai Orthobunyavirus.Pharmaceuticals (Basel, Switzerland) · 2026Article
- A computational method to design broad-spectrum T cell-inducing vaccines applied to Betacoronaviruses.Cell reports methods · 2026Article
- High-throughput in silico multi-epitope reverse vaccine design against hydatidosis.Scientific reports · 2026Article
- Broad-Spectrum Multi-Epitope Design Targeting Conserved Hantavirus Glycoproteins (Gn/Gc): Chimeric Antigen Engineering and Structural Mapping.International journal of molecular sciences · 2026Article
- Pocket restraints guided by B-cell epitope prediction improve Chai-1 antibody-antigen structure modeling.Protein science : a publication of the Protein Society · 2026Article
- Immunoinformatics-driven multi-epitope vaccine design as a promising strategy against multidrug-resistant pathogens: a comprehensive review.Folia microbiologica · 2026Review
- Establishment of an Indirect ELISA Detection Method for Porcine Circovirus 3 Based on Soluble Cap Protein.Veterinary sciences · 2026Article
117 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
B-cell epitope prediction tools are of great medical and commercial interest due to their practical applications in vaccine development and disease diagnostics. The introduction of protein language models (LMs), trained on unprecedented large datasets of protein sequences and structures, tap into a powerful numeric representation that can be exploited to accurately predict local and global protein structural features from amino acid sequences only. In this paper, we present BepiPred-3.0, a sequence-based epitope prediction tool that, by exploiting LM embeddings, greatly improves the prediction accuracy for both linear and conformational epitope prediction on several independent test sets. Furthermore, by carefully selecting additional input variables and epitope residue annotation strategy, performance was further improved, thus achieving unprecedented predictive power. Our tool can predict epitopes across hundreds of sequences in minutes. It is freely available as a web server and a standalone package at https://services.healthtech.dtu.dk/service.php?BepiPred-3.0 with a user-friendly interface to navigate the results.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.