Strategies for vaccine design for corona virus using Immunoinformatics techniques

Anamika Basu; Anasua Sarkar; Ujjwal Maulik

For docking studies, the T cell epitope PTDTYTSVY (MHC I restricted) and PTDTYTSVYLGKFRG (MHC II restricted) are selected and subjected to PEP-FOLD server [24] , [25] for 3D structure formation. To identify the molecular interactions with specific HLA protein for respective epitopes, docking studies are performed with ClusPro 2.2 web server [26] . Cluster scores for lowest binding energy prediction are calculated using the formula-E = 0.40E_{rep} + -0.40E_{att} + 600E_{elec} + 1.00E_{DARS}. Here, repulsive, attractive, electrostatic as well as interactions extracted from the decoys as the reference state, are considered for structure-based pairwise potential calculation in epitope-MHC molecule docking [27] . Modified PDB ID 4NQX for HLA-A*01:01 is used as allelic protein for docking study of T cell epitope with MHC I restricted. Similarly, 3D structure (PDB ID 1FV1) for HLA-DRB5*01:01 MHC molecule is used as receptor molecule for T cell epitope docking analysis with MHC II restriction.