Determination of binding site is important for understanding the function of biological macromolecules. Understanding the specific binding site of the substrate to the enzyme, which is called active site, is essential for investigating the mechanism of the enzyme. It is important to recognize the binding site of the hormone in the receptor, drug binding site in proteins and nucleic acids, etc. from different perspectives. In order to design new drugs, it is necessary to determine the drugs binding site in the macromolecule. There are several ways to investigate binding sites. Using X-ray and NMR are appropriate for this purpose. Fluorescence, Raman and IR methods can also be used. The use of molecules with a specific binding site is an indirect method for determining the binding site. For well-known structures that have PDB files, molecular docking techniques and molecular dynamics simulations it can be used.

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