ArticleBioinformatics (Oxford, England)2018
An automated benchmarking platform for MHC class II binding prediction methods.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers, 1 of them a synthesis that pooled it.
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Who cites it
57 citing papers in PubMed, 1 synthesis or guideline pooled it.
- In silico design of a T-cell epitope vaccine candidate for parasitic helminth infection.PLoS pathogens · 2020Pooled it
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- Immunopharmacologsical and structural insights into Rift Valley fever virus envelope glycoproteins: an immunoinformatics approach to multi-epitope vaccine design.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Cancer epitope prediction tools and analysis pipelines in CEDAR.Nucleic acids research · 2026Article
- Genome-Guided Discovery of Vaccine Targets for a Multi-Epitope Construct Against Multidrug-Resistant Enterobacter cloacae.MicrobiologyOpen · 2026Article
- The Cancer Epitope Database and Analysis Resource (CEDAR): current capabilities and future directions.Frontiers in oncology · 2026Review
- Artificial intelligence for coordinating vaccine design, antiviral discovery, and real-world monitoring in the era of emerging and endemic viral threats.Frontiers in pharmacology · 2026Review
- Computational methods and data resources for predicting tumor neoantigens.Briefings in bioinformatics · 2025Review
- Immunoinformatics method to design universal multi-epitope nanoparticle vaccine for TGEV S protein.Scientific reports · 2025Article
- Immunoinformatics design of an mRNA vaccine against classical swine fever virus using conserved E2 protein and NS3 T-lymphocyte epitopes.BioImpacts : BI · 2025Article
- An Immunoinformatic Approach for Identifying and Designing Conserved Multi-Epitope Vaccines for Coronaviruses.Biomedicines · 2024Article
- Epitopes screening and vaccine molecular design of PEDV S protein based on immunoinformatics.Scientific reports · 2024Article
- Subtractive Proteomics and Reverse-Vaccinology Approaches for Novel Drug Target Identification and Chimeric Vaccine Development againstBioengineering (Basel, Switzerland) · 2024Article
- Review
- MHCII-peptide presentation: an assessment of the state-of-the-art prediction methods.Frontiers in immunology · 2024Review
- Artificial intelligence-driven reverse vaccinology forFrontiers in molecular biosciences · 2024Article
- Bioactive Molecules from the Innate Immunity of Ascidians and Innovative Methods of Drug Discovery: A Computational Approach Based on Artificial Intelligence.Marine drugs · 2023Review
- Advances of Reverse Vaccinology for mRNA Vaccine Design against SARS-CoV-2: A Review of Methods and Tools.Viruses · 2023Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Motivation: Computational methods for the prediction of peptide-MHC binding have become an integral and essential component for candidate selection in experimental T cell epitope discovery studies. The sheer amount of published prediction methods-and often discordant reports on their performance-poses a considerable quandary to the experimentalist who needs to choose the best tool for their research. Results: With the goal to provide an unbiased, transparent evaluation of the state-of-the-art in the field, we created an automated platform to benchmark peptide-MHC class II binding prediction tools. The platform evaluates the absolute and relative predictive performance of all participating tools on data newly entered into the Immune Epitope Database (IEDB) before they are made public, thereby providing a frequent, unbiased assessment of available prediction tools. The benchmark runs on a weekly basis, is fully automated, and displays up-to-date results on a publicly accessible website. The initial benchmark described here included six commonly used prediction servers, but other tools are encouraged to join with a simple sign-up procedure. Performance evaluation on 59 data sets composed of over 10 000 binding affinity measurements suggested that NetMHCIIpan is currently the most accurate tool, followed by NN-align and the IEDB consensus method. Availability and implementation: Weekly reports on the participating methods can be found online at: http://tools.iedb.org/auto_bench/mhcii/weekly/. Contact: mniel@bioinformatics.dtu.dk. Supplementary information: Supplementary data are available at Bioinformatics online.
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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.