ArticleImmunogenetics2019
Improved peptide-MHC class II interaction prediction through integration of eluted ligand and peptide affinity data.
Article in Immunogenetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 2 of them syntheses that pooled it.
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Who cites it
28 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
- Challenges targeting cancer neoantigens in 2021: a systematic literature review.Expert review of vaccines · 2021Pooled it
- In silico design of a multiepitope vaccine against antibiotic drug-resistant Acinetobacter baumannii.Scientific reports · 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
- Preclinical evaluation of a CCL19 immune-potentiated DNA cancer vaccine.Cancer immunology, immunotherapy : CII · 2025Article
- On the impact of local protein structure features on prediction of major histocompatibility complex class I and II antigen presentation.Briefings in bioinformatics · 2025Article
- Advances in Therapeutic Cancer Vaccines, Their Obstacles, and Prospects Toward Tumor Immunotherapy.Molecular biotechnology · 2025Review
- RPEMHC: improved prediction of MHC-peptide binding affinity by a deep learning approach based on residue-residue pair encoding.Bioinformatics (Oxford, England) · 2024Article
- Therapeutic cancer vaccines: advancements, challenges, and prospects.Signal transduction and targeted therapy · 2023Review
- HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery.Immunity · 2023Article
- Does human homology reduce the potential immunogenicity of non-antibody scaffolds?Frontiers in immunology · 2023Review
- Bioinformatic Techniques for Vaccine Development: Epitope Prediction and Structural Vaccinology.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Integral Use of Immunopeptidomics and Immunoinformatics for the Characterization of Antigen Presentation and Rational Identification of BoLA-DR-Presented Peptides and Epitopes.Journal of immunology (Baltimore, Md. : 1950) · 2021Article
- A comparative analysis of SLA-DRB1 genetic diversity in Colombian (creoles and commercial line) and worldwide swine populations.Scientific reports · 2021Article
- Comparison of HLA ligand elution data and binding predictions reveals varying prediction performance for the multiple motifs recognized by HLA-DQ2.5.Immunology · 2021Article
- Improved prediction of HLA antigen presentation hotspots: Applications for immunogenicity risk assessment of therapeutic proteins.Immunology · 2021Article
- Citrullinated Epitopes Identified on Tumour MHC Class II by Peptide Elution Stimulate Both Regulatory and Th1 Responses and Require Careful Selection for Optimal Anti-Tumour Responses.Frontiers in immunology · 2021Article
- MS-Based HLA-II Peptidomics Combined With Multiomics Will Aid the Development of Future Immunotherapies.Molecular & cellular proteomics : MCP · 2021Review
- Thermostability profiling of MHC-bound peptides: a new dimension in immunopeptidomics and aid for immunotherapy design.Nature communications · 2020Article
- Toward Drug-Like Multispecific Antibodies by Design.International journal of molecular sciences · 2020Review
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Major histocompatibility complex (MHC) class II antigen presentation is a key component in eliciting a CD4+ T cell response. Precise prediction of peptide-MHC (pMHC) interactions has thus become a cornerstone in defining epitope candidates for rational vaccine design. Current pMHC prediction tools have, so far, primarily focused on inference from in vitro binding affinity. In the current study, we collate a large set of MHC class II eluted ligands generated by mass spectrometry to guide the prediction of MHC class II antigen presentation. We demonstrate that models developed on eluted ligands outperform those developed on pMHC binding affinity data. The predictive performance can be further enhanced by combining the eluted ligand and pMHC affinity data in a single prediction model. Furthermore, by including ligand data, the peptide length preference of MHC class II can be accurately learned by the prediction model. Finally, we demonstrate that our model significantly outperforms the current state-of-the-art prediction method, NetMHCIIpan, on an external dataset of eluted ligands and appears superior in identifying CD4+ T cell epitopes.
Indexed as
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31183519What OpenQuestion holds
Registered trials
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.