ArticleGenome medicine2018
Footprints of antigen processing boost MHC class II natural ligand predictions.
Article in Genome medicine, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers, 1 of them a synthesis that pooled it.
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Who cites it
53 citing papers in PubMed, 1 synthesis or guideline pooled it, 100 citations in OpenAlex.
- Challenges targeting cancer neoantigens in 2021: a systematic literature review.Expert review of vaccines · 2021Pooled it
- NetMHCIIphosPan: A Machine Learning Tool for Predicting HLA Class II Antigen Presentation of Phosphorylated Peptides.Journal of proteome research · 2026Article
- NetMHCIIphosPan: a machine learning tool for predicting HLA class II antigen presentation of phosphorylated peptides.bioRxiv : the preprint server for biology · 2026Article
- Beyond natural amino acids: extending immunogenicity risk assessment to modified peptides through chemical feature encoding. A case study on citrullination.Frontiers in immunology · 2026Article
- A superantigen-based MHC class II-targeted cancer immunotherapy for the treatment of acute myeloid leukemia.Blood cancer journal · 2025Article
- AstraMEV (AI-Guided Structural Assembly of Multi-Epitope Vaccines) Against Infectious Bronchitis Virus.Journal of chemical information and modeling · 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
- Development of a peptide-based vaccine using a T cell epitope derived from SARS-CoV-2.iScience · 2025Article
- Promiscuous class II-binding SARS-CoV-2-nuc derived vaccine-peptide induced extensive conventional, innate and unconventional T cell responses.Frontiers in immunology · 2025Article
- NetMHCpan-4.2: improved prediction of CD8+ epitopes by use of transfer learning and structural features.Frontiers in immunology · 2025Article
- New light on the HLA-DR immunopeptidomic landscape.Journal of leukocyte biology · 2024Article
- Graph-pMHC: graph neural network approach to MHC class II peptide presentation and antibody immunogenicity.Briefings in bioinformatics · 2024Article
- Structure-aware deep model for MHC-II peptide binding affinity prediction.BMC genomics · 2024Article
- RPEMHC: improved prediction of MHC-peptide binding affinity by a deep learning approach based on residue-residue pair encoding.Bioinformatics (Oxford, England) · 2024Article
- In Silico Tools for Predicting Novel Epitopes.Methods in molecular biology (Clifton, N.J.) · 2024Article
- An immunoinformatics study reveals a new BoLA-DR-restricted CD4+ T cell epitopes on the Gag protein of bovine leukemia virus.Scientific reports · 2023Article
- Accurate prediction of HLA class II antigen presentation across all loci using tailored data acquisition and refined machine learning.Science advances · 2023Article
- Structural Framework for Analysis of CD4+ T-Cell Epitope Dominance in Viral Fusion Proteins.Biochemistry · 2023Review
- Investigating the human and nonobese diabetic mouse MHC class II immunopeptidome using protein language modeling.Bioinformatics (Oxford, England) · 2023Article
- HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery.Immunity · 2023Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 4 countries.
Funding
Abstract
backgroundMajor histocompatibility complex class II (MHC-II) molecules present peptide fragments to T cells for immune recognition. Current predictors for peptide to MHC-II binding are trained on binding affinity data, generated in vitro and therefore lacking information about antigen processing.
methodsWe generate prediction models of peptide to MHC-II binding trained with naturally eluted ligands derived from mass spectrometry in addition to peptide binding affinity data sets.
resultsWe show that integrated prediction models incorporate identifiable rules of antigen processing. In fact, we observed detectable signals of protease cleavage at defined positions of the ligands. We also hypothesize a role of the length of the terminal ligand protrusions for trimming the peptide to the MHC presented ligand.
conclusionsThe results of integrating binding affinity and eluted ligand data in a combined model demonstrate improved performance for the prediction of MHC-II ligands and T cell epitopes and foreshadow a new generation of improved peptide to MHC-II prediction tools accounting for the plurality of factors that determine natural presentation of antigens.
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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 OpenQuestion graph.