ArticleMolecules (Basel, Switzerland)2018
The Utility of Supertype Clustering in Prediction for Class II MHC-Peptide Binding.
Article in Molecules (Basel, Switzerland), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Bioinformatic Tools for Studying the Cellular Immune Response to SARS-CoV-2, Vaccine Efficacy, and Future Pandemics at the Global Population Level.International journal of molecular sciences · 2024Review
- Conservation of HLA Spike Protein Epitopes Supports T Cell Cross-Protection in SARS-CoV-2 Vaccinated Individuals against the Potentially Zoonotic Coronavirus Khosta-2.International journal of molecular sciences · 2024Article
- Review
- Human leukocyte antigen-DQ risk heterodimeric haplotypes of left ventricular dysfunction in cardiac sarcoidosis: an autoimmune view of its role.Scientific reports · 2023Article
- Translational vaccinomics and structural filtration algorithm to device multiepitope vaccine for catastrophic monkeypox virus.Computers in biology and medicine · 2023Article
- Immunoinformatics-Based Identification of B and T Cell Epitopes in RNA-Dependent RNA Polymerase of SARS-CoV-2.Vaccines · 2022Article
- Prediction of Conserved HLA Class I and Class II Epitopes from SARS-CoV-2 Licensed Vaccines Supports T-Cell Cross-Protection against SARS-CoV-1.Biomedicines · 2022Article
- Predicted HLA Class I and Class II Epitopes From Licensed Vaccines Are Largely Conserved in New SARS-CoV-2 Omicron Variant of Concern.Frontiers in immunology · 2022Article
- Engineering a multi epitope vaccine against SARS-CoV-2 by exploiting its non structural and structural proteins.Journal of biomolecular structure & dynamics · 2022Article
- Functional characterization of CD4+ T cell receptors crossreactive for SARS-CoV-2 and endemic coronaviruses.The Journal of clinical investigation · 2021Article
- High throughput and comprehensive approach to develop multiepitope vaccine against minacious COVID-19.European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences · 2020Article
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Authors and funding
5 authors.
Funding
Abstract
motivationExtensive efforts have been devoted to understanding the antigenic peptides binding to MHC class I and II molecules since they play a fundamental role in controlling immune responses and due their involvement in vaccination, transplantation, and autoimmunity. The genes coding for the MHC molecules are highly polymorphic, and it is difficult to build computational models for MHC molecules with few know binders. On the other hand, previous studies demonstrated that some MHC molecules share overlapping peptide binding repertoires and attempted to group them into supertypes. Herein, we present a framework of the utility of supertype clustering to gain more information about the data to improve the prediction accuracy of class II MHC-peptide binding.
resultsWe developed a new method, called superMHC, for class II MHC-peptide binding prediction, including three MHC isotypes of HLA-DR, HLA-DP, and HLA-DQ, by using supertype clustering in conjunction with RLS regression. The supertypes were identified by using a novel repertoire dissimilarity index to quantify the difference in MHC binding specificities. The superMHC method achieves the state-of-the-art performance and is demonstrated to predict binding affinities to a series of MHC molecules with few binders accurately. These results have implications for understanding receptor-ligand interactions involved in MHC-peptide binding.
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