Molecular docking studies

Molecular docking was done using the GOLD software suite (Jones et al., 1997), a protein-ligand docking software to identify the ligand-binding pockets and allosteric sites in protein 3D molecule.The interaction between protein-ligand was analyzed with PyMOL v1.7.4.5. (http://www.pymol.org/), and LIGPLOT v.4.5.3 (https://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/) (Wallace, Laskowski & Thornton, 1995). The docking results were sorted according to the GOLD fitness score (GScore) and the complex with the highest score is considered to be the best docking complex and was considered for further analysis (Friesner et al., 2004). The GScore is calculated in Kcal/mol as:

Where, H bond: Hydrogen bonds, Lipo: hydrophobic interactions, Metal: metal-binding term, Site: polar interactions in the binding site, Coul: columbic forces, vdW: Vander-Waals forces, Bury P: penalty for buried polar group, RotB: freezing rotable bonds.