ArticleBiochemistry2022
CD4+ T-Cell Epitope Prediction by Combined Analysis of Antigen Conformational Flexibility and Peptide-MHCII Binding Affinity.
Article in Biochemistry, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed, 16 citations in OpenAlex.
- Quantifying Cross-Attention Interaction in Transformers for Interpreting TCR-pMHC Binding.ArXiv · 2026Article
- Article
- Conformational bias in SARS-CoV-2 Spike CD4+ T-cell epitope dominance.Frontiers in immunology · 2026Article
- AI-powered mapping of tumor immunity for optimized mRNA vaccine engineering.Frontiers in oncology · 2026Review
- Article
- AI-driven epitope prediction: a system review, comparative analysis, and practical guide for vaccine development.NPJ vaccines · 2025Review
- Clonal analysis of SepSecS-specific B and T cells in autoimmune hepatitis.The Journal of clinical investigation · 2025Article
- Structural Framework for Analysis of CD4+ T-Cell Epitope Dominance in Viral Fusion Proteins.Biochemistry · 2023Review
- NovelJournal of fungi (Basel, Switzerland) · 2023Article
- De novo design of anti-variant COVID-19 vaccine.Biology methods & protocols · 2023Article
- Massively-multiplexed epitope mapping techniques for viral antigen discovery.Frontiers in immunology · 2023Review
- Germline IgM predicts T cell immunity to Pneumocystis.JCI insight · 2022Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Antigen processing in the class II MHC pathway depends on conventional proteolytic enzymes, potentially acting on antigens in native-like conformational states. CD4+ epitope dominance arises from a competition among antigen folding, proteolysis, and MHCII binding. Protease-sensitive sites, linear antibody epitopes, and CD4+ T-cell epitopes were mapped in plague vaccine candidate F1-V to evaluate the various contributions to CD4+ epitope dominance. Using X-ray crystal structures, antigen processing likelihood (APL) predicts CD4+ epitopes with significant accuracy for F1-V without considering peptide-MHCII binding affinity. We also show that APL achieves excellent performance over two benchmark antigen sets. The profiles of conformational flexibility derived from the X-ray crystal structures of the F1-V proteins, Caf1 and LcrV, were similar to the biochemical profiles of linear antibody epitope reactivity and protease sensitivity, suggesting that the role of structure in proteolysis was captured by the analysis of the crystal structures. The patterns of CD4+ T-cell epitope dominance in C57BL/6, CBA, and BALB/c mice were compared to epitope predictions based on APL, MHCII binding, or both. For a sample of 13 diverse antigens, the accuracy of epitope prediction by the combination of APL and I-A
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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 Socratic graph.