With the Protein Preparation Wizard module, the proteins of dengue and herpes viruses were adjusted by removing the water molecules. In general, water molecule-containing proteins are not compatible for the molecular docking; therefore, water molecules were clean off from the proteins for further investigation. Two gears such as preparation and refinement were utilized during this process to detect water molecules and remove them from the proteins, while the workspace analyzer was aided to add the missing residues in the proteins. Later, the proteins were shifted for docking using two more gears: optimization and minimization. The entire target preparation process has been completed in accordance with our previous studies (Christy Rani et al. 2022 ; Kalaimathi et al. 2022 (link)).