T015: Protein-ligand docking. Next, we introduce molecular docking to predict the binding mode of a ligand to its protein target by explaining several sampling algorithms and scoring functions, as well as com-December 8, 2021 menting on limitations and interpretation of docking result. The theoretical background is then applied in a re-docking experiment aiming to reproduce the binding mode observed in a published X-ray structure of EGFR. Protein and ligand are prepared using Pybel , the ligand is docked into the protein using Smina , and finally, the docking poses can be visually inspected using NGLView . We refer to Jupy-terDock for further reading on different docking protocols run from Jupyter notebooks.