Molecular Docking with AutoDock Tools

Molecular docking was performed using AutoDock Tools 4.2.1 version^{88 (link)}. The polar hydrogen was added to the receptor (proteins) followed by addition of Kollman charges and computing Gasteiger charges. The torsions were calculated for respective ligands and both receptor and ligand files were saved as .pdbqt format. The grid optimization was performed using AutoGrid programme and the grid box was centered such that it covers all identified active pocket amino acid residues. Docking was carried out using AutoDock programme and ten different conformations were generated with respect to their binding energies. The energy values in AutoDock are calculated on basis of various intermolecular bonds such as- hydrogen bond, desolvation energy, van der Waals, and electrostatic energy, internal energy of ligand, and torsional free energy. Amongst these, the desolvation and van der Waals energy together forms the binding energy; the hydrogen bond and van der Waals energy forms the docking energy and the strength of binding of ligand to the receptor is determined by electrostatic interactions. Complexes having lowest binding energy were considered as the best receptor-ligand structure and were chosen for post docking analysis. The results were visualized using Discovery Studio Visualizer and MOE (Molecular Operating Environment) softwares.