2  Methodology

2.1  Protein retrieval and allergenicity analysis
Five protein sequences were selected from NCBI-GenBank, listed in Table 1 , for SARS-COV-2 based on their Allergenicity that relies on the Tanimoto similarity index score produced by AllergenFP 1.0 [8]. The selected proteins were the envelope protein, ORF3a protein, nucleocapsid phosphoprotein, ORF7a protein, and membrane glycoprotein, which are crucial for the structural integrity and functionality of the virus [38].
Table 1 List of proteins selected for SARS COV-2 with allergenicity.
Protein Gene Bank accession no. Protein name Allergen FP Score (Tanimoto similarity Index) Allergen/Non-Allergen
QHD43418.1 Envelop Protein 0.87 Non-Allergen
QHD43417.1 ORF3a Protein 0.84 Non-Allergen
QHD43423.2 Nulceocapsid Phosphoprotein 0.85 Non-Allergen
QHD43421.1 ORF7a protein 0.80 Non-Allergen
QHD43419.1 Membrane Glycoprotein 0.83 Non-Allergen

2.2  T-cell epitope prediction for MHC HLA alleles
IEDB (Immune epitope database) [20] along with NetMHCII PAN 3.2 and NETMHC 4.0 servers [18] were effectively used for finding putative peptide sequences that were aimed to interact with the MHC Class II and I HLA alleles, respectively (because of efficient algorithms based on artificial neural networks). The VaxiJen score is determined for screening the best antigenic epitopes using the VaxiJen online tool [10] with a threshold ≥ 1.0 for the viruses’ domain.

2.3  Structural prediction: Putative epitopes and MHC HLA alleles
The epitopes 3D structural findings were conducted by using the PEP-FOLD-3.5 server [25,33,34] and MHC HLA Allelic peptides tertiary or 3D structure were obtained from the RCSB-PDB database [4].

2.4  Molecular docking analysis
The selected epitopes and HLA complexes were docked for calculating refined interactions and binding energies, along with atomic contact energy (ACE), by using two docking web-servers: DINC 2.0 [2] and PatchDock [32].

2.5  Molecular dynamics-simulation analysis of docked complex
Molecular dynamics study was conducted to analyze RMSD values and atomic fluctuations for all amino acids under the 100 ps time frame by deploying the MDWeb server. MDWeb server was deployed to analyze Coarse grained MD Brownian dynamics (C-alpha) with specifications → Time: 100 ps, output frequency (steps) = 10, force constant (kcal/mol Ǻ2) = 40, distance between alpha carbon atoms(Ǻ) = 3.8 for both the interacting epitopes, and it was based on a GROMACS MD setup with solvation using an Amber-99sb* force-field [17].

2.6  Toxicity, Ramachandran-plot, and population coverage analysis
The ToxinPred server [16] is utilized for determining the toxicity scoring of Epitopes for selecting non-toxic ones; also, the Ramachandran plot analysis was deployed by using the MolProbity 4.2 server [6] to analyze the quantitative presence of residues in the favorable region.
The Immune Epitope Database (IED) resource web-server of population coverage was used to predict population coverage of the MHC II and MHC I alleles that interact with screened out epitopes based on their restriction database [5]. The MHCPred web-server was effectively used in quantitative prediction of sorted out epitopes interacting with HLA alleles of MHC II and MHC I [15]. Thereafter the ProtParam tool [42] of the ExPASy server was used to screen final stable epitopes based on the instability index and half-life.