ArticlePLoS computational biology2008
A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 456 papers, 1 of them a synthesis that pooled it.
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Who cites it
456 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Improving peptide vaccine manufacturability without sacrificing immunogenicity: substitution of methionine and cysteine with oxidation-resistant isosteres.Journal of immunology (Baltimore, Md. : 1950) · 2026Article
- Self-amplifying mRNA vaccine cocktail against Staphylococcus aureus: A multi-epitope immunoinformatics and structural simulation framework.World journal of microbiology & biotechnology · 2026Article
- Post-Translational Modifications Modulate the HLA-DR3 Restricted Epitope Landscape of Sjögren's Associated Autoantigens.Medicina (Kaunas, Lithuania) · 2026Article
- Cytokine-driven immunogenicity prediction: integrating HLA binding and cytokine induction.Briefings in bioinformatics · 2026Article
- Computational Design of an mRNA Vaccine Targeting LRP6 for Triple-Negative Breast Cancer Therapy.Cancer reports (Hoboken, N.J.) · 2026Article
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- Evaluating the effect of immunization with DNA encoding Phlebotomus sergenti apyrase protein (PsSP42) against Leishmania tropica infection in BALB/c mouse model.Parasites & vectors · 2026Article
- Generation and characterization of a novel MHC-II tetramer for tracking and characterization of toxin B-specific CD4bioRxiv : the preprint server for biology · 2026Article
- Clinical Serum-Anchored Computational Design Pipeline for a Broad-Spectrum Influenza Multi-Epitope mRNA Vaccine.Biology · 2026Article
- DSCA-HLAII: A dual-stream cross-attention model for predicting peptide-HLA class II interaction and presentation.PLoS computational biology · 2026Article
- Designing a multi-epitope vaccine against La Crosse virus using immunoinformatics approach.PloS one · 2026Article
- Designing a Multi-Epitope Vaccine Against NOTCH1 and NOTCH4: A Computational Approach for Triple-Negative Breast Cancer.BioMed research international · 2026Article
- Optimized Multi-Epitope Norovirus Vaccines Induce Robust Humoral and Cellular Responses in Mice.Vaccines · 2025Article
396 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
The identification of MHC class II restricted peptide epitopes is an important goal in immunological research. A number of computational tools have been developed for this purpose, but there is a lack of large-scale systematic evaluation of their performance. Herein, we used a comprehensive dataset consisting of more than 10,000 previously unpublished MHC-peptide binding affinities, 29 peptide/MHC crystal structures, and 664 peptides experimentally tested for CD4+ T cell responses to systematically evaluate the performances of publicly available MHC class II binding prediction tools. While in selected instances the best tools were associated with AUC values up to 0.86, in general, class II predictions did not perform as well as historically noted for class I predictions. It appears that the ability of MHC class II molecules to bind variable length peptides, which requires the correct assignment of peptide binding cores, is a critical factor limiting the performance of existing prediction tools. To improve performance, we implemented a consensus prediction approach that combines methods with top performances. We show that this consensus approach achieved best overall performance. Finally, we make the large datasets used publicly available as a benchmark to facilitate further development of MHC class II binding peptide prediction methods.
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