Ligand-protein Docking simulations

If structural information of the protein target is available, e.g., a crystal structure, in silico screening of huge virtual compound libraries can be conducted by the use of docking simulations. Based on identified primary hits, structural variations of the ligand can be evaluated by computational modeling of the ligand-protein complex. 

II. Docking simulation methods These are slower than the matching one, study the ligand outside the protein and randomly explore translations, orientations and conformations until an ideal site is found. 

Using information about the 3D shape of a protein receptor active site, which is derived from X-ray crystallography or NMR, ligands from the virtual library can be selected and fitted into the site. This is a modeling process known as docking simulation (Fig. 3.6). 

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