Table 2.

Selection of peptide antigens and T cell receptor–pMHC complex

P. no.	Peptide	Start position	Allele selection	Joint Z value	Best template	Domain
1	MDEFIERYKLEGY	6670	HLA-DR4	4.03	2ak4	ORF1ab polyprotein
2	PYEDFQENWNTKH	153	HLA-DR4	4.22	2ak4	ORF1a polyprotein
3	LQDVVNQNAQALN	948	HLA-DR4	4.12	2ak4	Surface glycoprotein-SPIKE
4	YDYCIPYNSVTSS	154	HLA-DR9	2.67	2ak4	ORF3a protein
5	YVYSRVKNLNSSR	1	HLA-DR4	0	2ak4	E protein
6	NGTITVEELKKLL	5	HLA-DR4	0	2ak4	Membrane glycoprotein
7	TENKYSQLDEEQP	45	HLA-DR4	0	2ak4	ORF6 protein
8	SPKLFIRQEEVQE	83	HLA-DR4	2.4	2ak4	ORF7a
9	FSLELQDHNETCH	30	HLA-DR4	1.97	2ak4	ORF7b
10	FYEDFLEYHDVRV	104	HLA-DR9	2.65	2ak4	ORF8
11	DQELIRQGTDYKH	288	HLA-DR4	3.42	2ak4	Nucleocapsid phosphoprotein
12	SRNYIAQVDVVNF	23	HLA-DR9	2.29	2ak4	ORF10

This table displays all predicted binders for specific pMHC allele in the single line just by highlighting the predicted binders. The starting residue of each predicted binder is shown in bold, while the rest of the residues in bold-italic