Secondly, as more and more structural information on possible protein targets and their biochemical role in the cell becomes available, completely new therapeutic concepts can be developed. Understanding the biological or biochemical mechanism of a disease then often suggests the types of molecules needed for new drugs. The central assumption is that a good fit results from structural and chemical complementarity to the target receptor. The techniques provided by computational methods include computer graphics for visualisation and the methodology of theoretical chemistry. By means of quantum mechanics the structure of small molecules can be predicted to experimental accuracy.
Statistical mechanics permits molecular motion and solvent effects to be incorporated.
Basically statistical mechanics is a three-dimensional equivalent of describing the position of billiard balls using Newton's law of motion. The best possible starting point is an X-ray crystal structure of the target site. If the molecular model of the binding site is precise enough, one can apply docking algorithms that simulate the binding of drugs to the respective receptor site. In a first step these programs create a negative image of the target site, as shown above , place the putative ligands into the site, as shown down below , and finally they evaluate the quality of the fit. Even if the structure of the receptor site is unknown the computer may help to figure out how it might look by comparing the chemical and physical properties of drugs that are known to act at a specific site.