The aptamer–RBD complex then underwent 100 ns molecular dynamic simulation using GROMACS 4.6.5 software packages [50]: CHARMM forcefield and SPC/E water model. The simulation system was neutralized by adding a suitable number of Na+/Cl ions. The solvated system was energy minimized in 1000 steps using steepest descent method iterations. After setting the temperature at 300 K and pressure at 1 bar, production simulation was run for 100 ns to evaluate dynamics of peptide aptamer, RBD of S-protein of SARS-CoV-2 as well as the aptamer–RBD complex. RMSD profile of peptide aptamer, RBD of S-protein of SARS-CoV-2 and aptamer–RBD complex and hydrogen-bonding profile of aptamer–RBD complex were studied.

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