3.7. In Silico Protein-Ligand Docking Simulation

Docking simulation is a computer simulation technique that is used to model the interaction between nuclear hormone receptors and their ligands. Among the many tools available for in silico protein-ligand docking, AutoDock4.2 is the most commonly used because of its automated docking capabilities. Ligand docking was performed using a set of predefined three-dimensional (3D) grids of the target protein and a systemic search technique. To prepare for the docking procedure, the following procedures were performed: (1) two-dimensional (2D) structures were converted into 3D structures; (2) charges were calculated; and (3) hydrogen atoms were added using the ChemOffice program (http://www.cambridgesoft.com).