PMC:7519301 / 45564-46830 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7519301","sourcedb":"PMC","sourceid":"7519301","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7519301","text":"Prediction of CD4+ and CD8+ T Cell Epitopes.\nCD4+ and CD8+ T cell epitopes were predicted for four SARS-CoV-2 structural proteins: S (accession YP_009724390), N (accession YP_009724397), M (accession YP_009724393), and E (accession YP_009724392). CD4+ T cell epitopes were predicted using a server that predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks, NetMHCIIPan 4.0 (64) with a peptide length of 15. MHC class II HLA alleles of HLA-DQB1, plus the haplotypes of HLA-DPA1-DPB1 and HLA-DQA1-DPB, were selected for predictions if they had frequencies of \u003e1/1,000 in known allele/haplotype distributions (http://17ihiw.org/17th-ihiw-ngs-hla-data/). If multiple peptides had the same core, the peptide with the strongest binding score was selected for analysis. CD8+ T cell epitopes were predicted using NetMHCPan 4.1 (64) with a peptide length of 9. MHC class I HLA alleles of HLA-A, HLA-B, and HLA-C were selected if they were classified as common (frequency ≥ 1/10,000) in any of the populations in the database CIWD 3.0 (Common, Intermediate and Well-Documented HLA Alleles in World Populations) (65). Epitopes predicted as strong binders (with predicted binding affinities below 50 nM) were selected for 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