Design of multi epitope-based peptide vaccine against E protein of human COVID-19: An immunoinformatics approach

Miyssa I. Abdelmageed; Abdelrahman H. Abdelmoneim; Mujahed I. Mustafa; Nafisa M. Elfadol; Naseem S. Murshed; Shaza W. Shantier; Abdelrafie M. Makhawi

Molecular docking was performed using Autodock 4.0 software, based on Lamarckian Genetic Algorithm; which combines energy evaluation through grids of affinity potential to find the suitable binding position for a ligand on a given protein [54, 55] Polar hydrogen atoms were added to the protein targets and Kollman united atomic charges were computed. The target's grid map was calculated and set to 60×60×60 points with grid spacing of 0.375 Ǻ . The grid box was then allocated properly in the target to include the active residue in the center. The genetic algorithm and its run were set to 100.The docking algorithms were set to default. Finally, results were . CC-BY-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.04.934232 doi: bioRxiv preprint retrieved as binding energies and poses that showed lowest binding energies were visualized using UCSF Chimera.