ArticleJournal of immunology (Baltimore, Md. : 1950)2012
The utility and limitations of current Web-available algorithms to predict peptides recognized by CD4 T cells in response to pathogen infection.
Article in Journal of immunology (Baltimore, Md. : 1950), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 62 citations in OpenAlex.
- CD11a and CD49d enhance the detection of antigen-specific T cells following human vaccination.Vaccine · 2017Trial
- Immunoinformatics-driven multi-epitope vaccine design as a promising strategy against multidrug-resistant pathogens: a comprehensive review.Folia microbiologica · 2026Review
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- Systematic identification of minor histocompatibility antigens predicts outcomes of allogeneic hematopoietic cell transplantation.Nature biotechnology · 2025Article
- copepodTCR: Identification of Antigen-Specific T Cell Receptors with combinatorial peptide pooling.bioRxiv : the preprint server for biology · 2024Article
- CD4+ T-Cell Epitope Prediction by Combined Analysis of Antigen Conformational Flexibility and Peptide-MHCII Binding Affinity.Biochemistry · 2022Article
- Antitumor Peptide-Based Vaccine in the Limelight.Vaccines · 2022Review
- Identification of Immunogenic MHC Class II Human HER3 Peptides that Mediate Anti-HER3 CD4Cancer immunology research · 2022Article
- Detection of IFNγ-Secreting CD4Viruses · 2021Article
- Improved prediction of HLA antigen presentation hotspots: Applications for immunogenicity risk assessment of therapeutic proteins.Immunology · 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
- Immune Complex Formation Is Associated With Loss of Tolerance and an Antibody Response to Both Drug and Target.Frontiers in immunology · 2021Article
- epitopepredict: a tool for integrated MHC binding prediction.GigaByte (Hong Kong, China) · 2021Article
- Bioinformatic HLA Studies in the Context of SARS-CoV-2 Pandemic and Review on Association of HLA Alleles with Preexisting Medical Conditions.BioMed research international · 2021Review
- T Cell Epitope Predictions.Annual review of immunology · 2020Review
- CD4 T Cell Determinants in West Nile Virus Disease and Asymptomatic Infection.Frontiers in immunology · 2020Article
- Peptide Epitope Hot Spots of CD4 T Cell Recognition Within Influenza Hemagglutinin During the Primary Response to Infection.Pathogens (Basel, Switzerland) · 2019Article
- Computational prediction of vaccine potential epitopes and 3-dimensional structure of XAGE-1b for non-small cell lung cancer immunotherapy.Biomedical journal · 2018Article
- Determination of a Predictive Cleavage Motif for Eluted Major Histocompatibility Complex Class II Ligands.Frontiers in immunology · 2018Article
- Profiling the Targets of Protective CD8Molecular therapy. Methods & clinical development · 2017Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
The ability to track CD4 T cells elicited in response to pathogen infection or vaccination is critical because of the role these cells play in protective immunity. Coupled with advances in genome sequencing of pathogenic organisms, there is considerable appeal for implementation of computer-based algorithms to predict peptides that bind to the class II molecules, forming the complex recognized by CD4 T cells. Despite recent progress in this area, there is a paucity of data regarding the success of these algorithms in identifying actual pathogen-derived epitopes. In this study, we sought to rigorously evaluate the performance of multiple Web-available algorithms by comparing their predictions with our results--obtained by purely empirical methods for epitope discovery in influenza that used overlapping peptides and cytokine ELISPOTs--for three independent class II molecules. We analyzed the data in different ways, trying to anticipate how an investigator might use these computational tools for epitope discovery. We come to the conclusion that currently available algorithms can indeed facilitate epitope discovery, but all shared a high degree of false-positive and false-negative predictions. Therefore, efficiencies were low. We also found dramatic disparities among algorithms and between predicted IC(50) values and true dissociation rates of peptide-MHC class II complexes. We suggest that improved success of predictive algorithms will depend less on changes in computational methods or increased data sets and more on changes in parameters used to "train" the algorithms that factor in elements of T cell repertoire and peptide acquisition by class II molecules.
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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.