Adam B Shapiro
Does your question refer to the identification of the binding site on a protein of a low-molecular weight ligand? Ideally, this is done by solving the 3-D structure of the protein with ligand bound using x-ray crystallography or multidimensional NMR.
If you want to identify the amino acid residue(s) on a protein with which a reactive compound reacts but don't need to have the 3-D structure, you can use peptide mapping by LC-MS.
If you just need to know whether or not the ligand binds in the active site of an enzyme or the ligand binding site of a receptor, you can test for competitive binding with a known substrate, inhibitor, or ligand.
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