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The peptides from the proteome of H5N1 virus which are predicted to bind to different HLAs, do not show similarity with peptides of human proteome and are also identified to be generated by proteolytic cleavage.
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The average predicted binding affinity for ligands restricted to different HLA alleles is often very different.
Each HLA allotype binds to different ligands characterized by specific binding motifs [ 91].
These peptides can bind different HLA-DRB1 alleles, as established according to the SYFPEITHI site (www.syfpeithi.de).syfpeithi.de
Thus, the crystal structure of LILRA3 D1 clearly indicates that LILRA3 would bind to both HLA-A*0201 HLA-A*0201.
The HMM model that was trained by HLA-DQ2 showed significantly low likelihood values to peptides that bind to eight HLA-DR molecules.
Of these sequences, 62 contained nonamers predicted to bind to multiple HLA supertypes.
Our group has recently identified conserved CD4 epitopes from HIV that were able to bind to multiple HLA-DR molecules.
Importantly, all analogues bind to the HLA-A2 molecule with identical affinities 6.
For example, various peptide fragments can bind to human HLA-A2 Class I MHC molecules [ 39].
Immunisation with peptides predicted to bind to HLA-DR4 also induces T-cell responses in HLA-DR4 transgenic mice [ 2].
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