Abbas Alibakhshi - Molecular Medicine Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
Armina Alagheband Bahrami - Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Science, Tehran, Iran
Elmira Mohammadi - Core Research Facilities, Isfahan University of Medical Sciences, Isfahan, Iran- Applied Physiology Research Center, Cardiovascular Research Institute, Isfahan University of MedicalSciences, Isfahan, Iran
Shahrzad Ahangarzadeh - Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences,Isfahan, Iran
Meysam Mobasheri - Department of Biotechnology, Faculty of Advanced Sciences and Technology, Tehran Islamic AzadUniversity of Medical Sciences, Tehran, Iran

Frequent and sometimes more dangerous mutations in the SARS-CoV-۲ indicate that a stronger strategy isneeded to produce an effective vaccine. A vaccine that contains a wider range of virus factors and remainseffective if one or more mutations is happen in a part of the genome. In this study, four important virusproteins, S, E, M and Mpro were used to make a multi-epitope protein vaccine. For this purpose, thesequences were retrieved from NCBI gene database and then antigenic determinant of ۴ proteins using IEDB,MHCpred, ProPred, RANKPEP, ABCpred, BCpreds, BepiPred, Ellipro servers were selected and a proteinstructure was designed using ۴ domains containing epitopes. After examining its antigenic and allergenicitypotential usingVaxiJen v۲.۰ server AllerTOP v۲.۰ server respectively, its three-dimensional structure wasdesigned by two servers, Robetta and I-TASSER and then it was docked with immune system receptors usingAutodock vina program embedded in the PyRx software. Finally, using the dynamic molecular method byGromacs package ۵.۱.۱, complexes and interactions were investigated and their interaction energies weremeasured. The results of the study showed that the designed structure has good relative stability and interactswell with its receptors and can be used as a vaccine candidate for further studies.

SARS-CoV-۲; Covid-۱۹; Multi-epitope; Vaccine; Molecular docking; Molecular dynamics