ArticlePloS one2010
Limitations of Ab initio predictions of peptide binding to MHC class II molecules.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Challenges targeting cancer neoantigens in 2021: a systematic literature review.Expert review of vaccines · 2021Pooled it
- Review
- Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens.Journal of chemical theory and computation · 2023Review
- Computationally-Aided Modeling of Hsp70-Client Interactions: Past, Present, and Future.The journal of physical chemistry. B · 2022Article
- Article
- The pockets guide to HLA class I molecules.Biochemical Society transactions · 2021Review
- Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide Binders.Frontiers in molecular biosciences · 2021Article
- MHCII3D-Robust Structure Based Prediction of MHC II Binding Peptides.International journal of molecular sciences · 2020Article
- A Pan-Specific GRU-Based Recurrent Neural Network for Predicting HLA-I-Binding Peptides.ACS omega · 2020Article
- Immunoinformatics: Predicting Peptide-MHC Binding.Annual review of biomedical data science · 2020Article
- T Cell Epitope Predictions.Annual review of immunology · 2020Review
- Computer-aided prediction of antigen presenting cell modulators for designing peptide-based vaccine adjuvants.Journal of translational medicine · 2018Article
- Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition.PloS one · 2018Article
- Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes.Current topics in medicinal chemistry · 2018Review
- VaccineDA: Prediction, design and genome-wide screening of oligodeoxynucleotide-based vaccine adjuvants.Scientific reports · 2015Article
- Machine Learning Methods for Predicting HLA-Peptide Binding Activity.Bioinformatics and biology insights · 2015Review
- Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions.BMC bioinformatics · 2013Article
- PREDIVAC: CD4+ T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity.BMC bioinformatics · 2013Article
- The utility and limitations of current Web-available algorithms to predict peptides recognized by CD4 T cells in response to pathogen infection.Journal of immunology (Baltimore, Md. : 1950) · 2012Article
- Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy?Expert review of vaccines · 2012Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Successful predictions of peptide MHC binding typically require a large set of binding data for the specific MHC molecule that is examined. Structure based prediction methods promise to circumvent this requirement by evaluating the physical contacts a peptide can make with an MHC molecule based on the highly conserved 3D structure of peptide:MHC complexes. While several such methods have been described before, most are not publicly available and have not been independently tested for their performance. We here implemented and evaluated three prediction methods for MHC class II molecules: statistical potentials derived from the analysis of known protein structures; energetic evaluation of different peptide snapshots in a molecular dynamics simulation; and direct analysis of contacts made in known 3D structures of peptide:MHC complexes. These methods are ab initio in that they require structural data of the MHC molecule examined, but no specific peptide:MHC binding data. Moreover, these methods retain the ability to make predictions in a sufficiently short time scale to be useful in a real world application, such as screening a whole proteome for candidate binding peptides. A rigorous evaluation of each methods prediction performance showed that these are significantly better than random, but still substantially lower than the best performing sequence based class II prediction methods available. While the approaches presented here were developed independently, we have chosen to present our results together in order to support the notion that generating structure based predictions of peptide:MHC binding without using binding data is unlikely to give satisfactory results.
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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.