2.6.1. Preparation of Small-Molecule Ligands

To better evaluate the reliability of the network predictions, the core active ingredients were then molecularly docked to the core gene targets. First, small-molecule ligands were prepared by obtaining the 2D structures of their active ingredients in the sdf format through the PubChem database (https://pubchem.ncbi.nlm.nih.gov/) and then converting the 2D structures into 3D structures in the mol2 format through ChemOffice software. Finally, the results were imported into AutoDockTools to convert to files into the pdbqt format [28].