4.6.3. Validation of the Molecular Docking Method

Molecular docking validation was carried out using AutoDock Tools 1.5.6 by redocking a native ligand against a target protein that had had its natural ligand removed. Water ligands contained in the protein receptor were removed by adjusting the position of the grid box on the native ligand, which was then docked. The process was carried out to determine the RMSD value; native ligand redocking was considered successful if the RMSD value was <2 Å [51], which was obtained by looking at the overlay of the native ligand that was separated before docking, and the redocked validation of native ligand using Discovery Studio Visualizer.