ArticleBriefings in bioinformatics2023
epitope1D: accurate taxonomy-aware B-cell linear epitope prediction.
Article in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Isolation and Genomic Characteristics of the First Bovine Viral Diarrhea Virus Subgenotype 2b Isolate from Buffalo in Guangxi Province, China.Microorganisms · 2026Article
- Article
- Phylogenetic Domain Adaption for Linear B-Cell Epitope Prediction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- BLMPred: Predicting linear B-cell epitopes using pre-trained protein language models and machine learning.Computational and structural biotechnology journal · 2026Article
- Computational identification of B- and T-cell epitopes: a unified task taxonomy and review of databases, datasets, predictive pipelines, and gaps.Frontiers in immunology · 2026Review
- 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
- Complete gene sequence diversity, amplification, and natural selection of the Plasmodium vivax Duffy binding protein locus.Malaria journal · 2025Article
- Homology Modeling of Sesame Allergenic Protein and Prediction of B-Cell Linear Antigenic Epitopes Using Immunoinformatic Tools.Foods (Basel, Switzerland) · 2025Article
- Computational Methods in Immunoinformatics: Epitope Discovery and Diagnostic Applications.ACS omega · 2025Review
- A novel mRNA-based multi-epitope vaccine for rabies virus computationally designed via reverse vaccinology and immunoinformatics.Scientific reports · 2025Article
- Subtractive proteomics and reverse-vaccinology approaches for novel drug targets and designing a chimeric vaccine againstFrontiers in immunology · 2025Article
- Epitope-based antibody development against metalloproteinases and phospholipases AThe journal of venomous animals and toxins including tropical diseases · 2025Article
- Advances of computational methods enhance the development of multi-epitope vaccines.Briefings in bioinformatics · 2024Review
- Phylogeny-aware linear B-cell epitope predictor detects targets associated with immune response to orthopoxviruses.Briefings in bioinformatics · 2024Article
- Comparative membrane proteomic analysis of Tritrichomonas foetus isolates.Scientific reports · 2024Article
- piscesCSM: prediction of anticancer synergistic drug combinations.Journal of cheminformatics · 2024Article
- The rise of taxon-specific epitope predictors.Briefings in bioinformatics · 2024Article
- Single-residue linear and conformational B cell epitopes prediction using random and ESM-2 based projections.Briefings in bioinformatics · 2024Article
- Integrating machine learning to advance epitope mapping.Frontiers in immunology · 2024Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ability to identify B-cell epitopes is an essential step in vaccine design, immunodiagnostic tests and antibody production. Several computational approaches have been proposed to identify, from an antigen protein or peptide sequence, which residues are more likely to be part of an epitope, but have limited performance on relatively homogeneous data sets and lack interpretability, limiting biological insights that could otherwise be obtained. To address these limitations, we have developed epitope1D, an explainable machine learning method capable of accurately identifying linear B-cell epitopes, leveraging two new descriptors: a graph-based signature representation of protein sequences, based on our well-established Cutoff Scanning Matrix algorithm and Organism Ontology information. Our model achieved Areas Under the ROC curve of up to 0.935 on cross-validation and blind tests, demonstrating robust performance. A comprehensive comparison to alternative methods using distinct benchmark data sets was also employed, with our model outperforming state-of-the-art tools. epitope1D represents not only a significant advance in predictive performance, but also allows biologically meaningful features to be combined and used for model interpretation. epitope1D has been made available as a user-friendly web server interface and application programming interface at https://biosig.lab.uq.edu.au/epitope1d/.
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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.