The root-mean-square deviation (RMSD) variations obtained from the re-docking calculations suggested that the program correctly and efficiently simulated the experimental results for the respective ligands. RMSD values were 0.55 Ǻ for native and mutant M pro , 1.64 Ǻ for DNA gyrase and 1.91 Ǻ for cutinase. These preliminary results indicate that the conformational shift of the molecular docking technique is suitable for this study, and that the method is highly sensitive and specific. The re-docking overlay is shown in shows the intermolecular interaction energies for these compounds at M pro binding site (native and mutant), DNA gyrase, and cutinase.