4.10.1. Protein Preparation

For docking studies, three-dimensional structures of anti-apoptotic proteins, such as BCL-2 and CASPASE-3, were retrieved from the RCSB PDB protein data bank [57,58], with their respective PDB ID (4LVT and 3DEK). For docking simulations, water molecules and free hydrogen atoms were removed, and polar molecules were added to all protein structures using the pymol tool and automated AutoDock tool. Further active sites were analyzed in protein receptors using the web-based online tool Q-SiteFinder. All ions, except for the binding site, and non-relevant crystallographic materials were removed. These active sites were chosen as the most favorable binding residues for our docking simulation.
