Docking is a modeling process in which the interactions between molecules are examined.
Preparation for docking involves the modeling and experimental techniques we have discussed earlier in the course. For example, the structure of the macromolecule, which we will refer to as the receptor, must be determined. Ideally, we will have structural information from X-ray diffraction or NMR, though a good homology model also could be used. The structure of the small molecule, the ligand, also is required. A model-built structure may be used, though extensive conformational searching should be done.