SURFNET can help locate and visualize a protein's binding site.
This is done by computing all of the protein's gap regions (ie its clefts and cavities), as shown for dihydrofolate reductase (PDB code 3dfr).
The gap regions include all the protein's internal cavities and surface grooves. The binding site is usually the largest of the gap regions and can be extracted by a program called MASK.
The following show close-ups of the thermolysin binding site (PDB code 4tmn), with 3 ligands superposed (from 4tmn, 1tmn and 1tlp):-
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