2.6.2. Induced-fit docking

Considering the fact that rigid docking has some limitations as the protein is kept rigid [^37,38], the accuracy of its results has to be further evaluated. The induced-fit docking module of Schrödinger was utilized to accomplish induced-fit docking [^39,40]. In brief, the ligand is docked into the active site of the protein utilizing the Glide protocol (SP) [⁴¹], while the active site residues of the protein are maintained rigid. Next, the protein side chains or backbone are refined using the prime refinement module [^42,43]. Finally, the ligand is redocked into the refined protein conformation, and the score is calculated to rank the protein-ligand complex. The centroid of the residues was selected for the box center option, and the residues of active sites were selected. For the conformational sampling option, the sample ring conformation was chosen with the energy window of 2.5 kcal/mol. The receptor van der Waals scaling and the ligand van der Waals scaling were set to 0.7 and 0.5, respectively. The residues were refined within 5 Å of the ligand poses, and Glide redocking was performed on the structures within 30 kcal/mol of the best structure.