PMC:7111504 / 20194-21502 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7111504","sourcedb":"PMC","sourceid":"7111504","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7111504","text":"Predicting cross reactivity to 1G4 TCR\nTo gauge the level of 1G4 TCR cross-reactivity to list of 2019-nCoV virus, we have leveraged the data from a recently published study 7. 1G4 or NY-ESO-1-specific TCR is a very well-studied and clinically efficacious TCR which recognize the peptide ‘SLLMWITQC’ presented by HLA-A*02:01. Karapetyan et al. have recently provided data from three experimental assays reflecting Binding, Activating and Killing upon each mutation at each position of all possible 9-mers using these three datasets. In a similar way to the original paper, we trained three Position Weight Matrices named B, A and K respectively from Binding, Activating and Killing assay. We defined the cross-reactivity score of a given 9-mer sequence as the geometric mean of B, A and K.\nWe then scanned 2019-nCoV virus protein sequence with each of B, A and K PWMs and associated each of 9613 9-mers with a cross reactivity score. At the same we utilized NetMHCpan and associated each 9-mer with its presentation score. Our final list of cross-reactive candidate peptides were those with a cross-reactivity sore \u003e= 0.8 and reported as strong binders from NetMHCpan and have ‘L’ and ‘V’ amino acids at anchor positions. The custom R codes are accessible from GitHub repository (see software availability 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