Epitopes prediction
The Immune Epitope Database and Analysis Resource (IEDB), NetMHC4.0
Server and NetMHCpan 4.1 Server are used to predict binding of peptides
to MHC molecule of known sequence using artificial neural networks
(ANNs). Specifically, nine-mer peptide as the peptide length option was
selected. HLA-E*0101 or HLA-E*0103-restricted SARS-CoV-2 nine-mer
peptide epitopes were predicted by inputting 1,273 amino acids of S
protein sequence, 75 amino acids of E protein sequence, 222 amino acids
of M protein sequence and 419 amino acids of N protein sequence of
SARS-CoV-2 prototype strain Wuhan-Hu-1 (GenBank accession number:
NC_045512.2) into the databases, respectively.
There is only HLA-E*0101 allele option could be selected in NetMHC4.0
Server database, while both HLA-E*0101 and E*0103 alleles could be
selected in NetMHCpan 4.1 Server database under the loci or species
option with HLA-E. Both the two methods specified if a sequence is a
strong MHC binder (SB) or a weak MHC binder (WB) based on a %Rank
score. By default, %Rank < 0.5% and %Rank < 2%
thresholds are considered for detecting as SB and WB for HLA-E molecule.