ArticleJournal of proteome research2018
Improved Prediction of Bovine Leucocyte Antigens (BoLA) Presented Ligands by Use of Mass-Spectrometry-Determined Ligand and in Vitro Binding Data.
Article in Journal of proteome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 50 citations in OpenAlex.
- 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
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- HLAIIPred: cross-attention mechanism for modeling the interaction of HLA class II molecules with peptides.Communications biology · 2025Article
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- Predicting MHC-I ligands across alleles and species: how far can we go?Genome medicine · 2025Article
- Immunopeptidomics ofBiology · 2024Article
- Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification.Molecular & cellular proteomics : MCP · 2024Review
- Selection of vaccine-candidate peptides fromFrontiers in immunology · 2024Article
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- Therapeutic Vaccines Targeting Neoantigens to Induce T-Cell Immunity against Cancers.Pharmaceutics · 2022Review
- Systematic Determination of TCR-Antigen and Peptide-MHC Binding Kinetics among Field Variants of aJournal of immunology (Baltimore, Md. : 1950) · 2022Article
- Peptidomes and Structures Illustrate How SLA-I Micropolymorphism Influences the Preference of Binding Peptide Length.Frontiers in immunology · 2022Article
- Comparing Class II MHC DRB3 Diversity in Colombian Simmental and Simbrah Cattle Across Worldwide Bovine Populations.Frontiers in genetics · 2022Article
- Nanovaccines against Animal Pathogens: The Latest Findings.Vaccines · 2021Review
- Proteome-wide analysis of Coxiella burnetii for conserved T-cell epitopes with presentation across multiple host species.BMC bioinformatics · 2021Article
- 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
- Improved prediction of HLA antigen presentation hotspots: Applications for immunogenicity risk assessment of therapeutic proteins.Immunology · 2021Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Peptide binding to MHC class I molecules is the single most selective step in antigen presentation and the strongest single correlate to peptide cellular immunogenicity. The cost of experimentally characterizing the rules of peptide presentation for a given MHC-I molecule is extensive, and predictors of peptide-MHC interactions constitute an attractive alternative. Recently, an increasing amount of MHC presented peptides identified by mass spectrometry (MS ligands) has been published. Handling and interpretation of MS ligand data is, in general, challenging due to the polyspecificity nature of the data. We here outline a general pipeline for dealing with this challenge and accurately annotate ligands to the relevant MHC-I molecule they were eluted from by use of GibbsClustering and binding motif information inferred from in silico models. We illustrate the approach here in the context of MHC-I molecules (BoLA) of cattle. Next, we demonstrate how such annotated BoLA MS ligand data can readily be integrated with in vitro binding affinity data in a prediction model with very high and unprecedented performance for identification of BoLA-I restricted T-cell epitopes. The prediction model is freely available at http://www.cbs.dtu.dk/services/NetMHCpan/NetBoLApan . The approach has here been applied to the BoLA-I system, but the pipeline is readily applicable to MHC systems in other species.
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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.