The Essential Facts of Wuhan Novel Coronavirus Outbreak in China and Epitope-based Vaccine Designing against COVID-19

Bishajit Sarkar; Md. Asad Ullah; Fatema Tuz Johora; Masuma Afrin Taniya; Yusha Araf

In this step, peptide-protein docking was performed to predict the binding of epitopes with various antibodies or the MHC receptors [122] . The molecular docking study of the epitopes were conducted using PatchDock (https://bioinfo3d.cs.tau.ac.il/PatchDock/php.php) server against HLA-A*11-01 allele (PDB ID: 5WJL) and HLA DRB1*04-01 (PDB ID: 5JLZ). PatchDock tool is a quick, easy, efficient and effective online docking tool which works on some specific algorithms. These algorithms divide the connolly dot surface representations of the compounds into concave, convex and flat patches. Later, possible solutions are predicted from these patches and RMSD (root mean square deviation) scores are applied to the candidate solutions. Based on the RMSD scores, the best candidate solutions are determined by the server. After successful docking by PatchDock, the refinement and re-scoring of the docking results were carried out by the FireDock server (http://bioinfo3d.cs.tau.ac.il/FireDock/php.php). The FireDock server generates global energies for the best solutions and the lowest global energy is always considered as the best docking score [113]- [126] . The best results were visualized using Discovery Studio Visualizer [127] .