Fig. 5

Visualization of epitope-receptor binding by use of ClusPro molecular docking. Panel A: a docked complex of a representative putative epitope (DENV4 NS3 ₃₃₅YQGKTVWFV₃₆₃) and HLA-A2*0201 receptor (PDB ID: 2GIT). Panel B: docked control, known peptide-HLA complex (PDB ID: 3SPV). Peptide in either complex is represented by a cyan ‘New Cartoon’ structure, while HLA receptor is represented by a silver transparent ‘QuickSurf’ and ‘New Cartoon’ (chain α: purple; chain β: yellow). The inset in panel A shows two interactions between the epitope and the HLA receptor (chain α1: blue ‘QuickSurf’ background; chain α2: red ‘QuickSurf’ background) within the cut-off distance of 5.0 Å, which are 4.30 Å and 4.72 Å