Motivation Finding out the similarites between molecules is essential to many areas of academic and industrial biology. Drug design requires the ability to recognize whether a given molecule has the required structure for a protein. To do this, companies determine the location of sites on proteins that potential drugs need to bind to, and then search a databases of molecules to find one that has the necessary structure. One large difficulty is determining what structure these small molecules must have in order to achieve the desired results. Another major difficulty comes from the flexibility of molecules.
Molecules can exist in many conformations, depending on torsional angles, temperature, and presure.