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. Docking of several conformers of the ligand with the receptor may be advisable.
Docking can proceed after the structures are available.
Also provided at their Web site is a description of the DOCK algorithm. DOCK is based on a sphere matching procedure and allows partial ligand flexibility. Another docking program is AutoDock . It applies simulated annealing to the docking process, allowing several torsional degrees of freedom in a flexible ligand to be searched. In addition, an automated docking algorithm, FlexX , is currently available for use over the WWW for free.