2.6. Molecular Docking Verification

In this study, molecular docking method was preliminarily utilized to validate the results of network pharmacology. Through the RCSB Protein Data Bank (PDB, http://www.rcsb.org/pdb), protein receptors of hub genes were selected according to the following criteria: (1) the structure of protein receptors was identified by X-ray diffraction, (2) X-ray resolution < 3 as the first choice, and (3) protein structures containing original ligands (e.g., inhibitors) were preferred. By using AutoDockTools1.5.6 (http://autodock.scripps.edu), the original ligands (if any), excess protein chains, and water molecules of the protein receptor were removed, then hydrogen was added to the protein receptors, and possible docking coordinates were searched. The structure (“mol2” format) of the corresponding bioactive ingredients of the target protein was obtained by TCMSP database. Subsequently, the file format of protein receptor or bioactive ingredient was converted to “PDBQT” using AutoDockTools, and molecular docking was performed using AutoDock Vina program (http://vina.scripps.edu/). Finally, the results were analyzed and visualized using PyMOL (http://www.pymol.org/) and Discovery Studio 2016.