Proteins can roughly be considered as a chain consisting of amino acids. Each amino acid contains a functional group and the so-called rest. Such a rest of an amino acid is called side chain. The formation of a chain happens at the functional group, where two amino acids are linked together by a peptide bond. This can theoretically be performed to an arbitrary extent. The different types of amino acids are generally abbreviated by a 3-letter code. When specifying a protein, it suffices to denote its amino acid sequence.
The theoretical determination of the interactions between two proteins or a protein and a ligand respectively, roughly spoken of as their binding, is of great interest since it allows for the verification of hypotheses stated during the so-called process of drug design without being reliant on experiments in laboratory. A recurrent problem is the so-called protein-protein-docking which is defined as follows:
Given the spatial structures of two proteins A and B, which are known to form a complex AB, then the protein-protein-docking is defined as the correct prediction of the complex structure AB.
There are different approaches to the problem of protein-protein-docking. The easiest one considers proteins to be rigid structures. This approach is called rigid body docking (RBD). It is based on the lock-and-key-principle, which was proposed by Emil Fischer in 1894.
This model treats the proteins that are to be docked, in his case an enzyme and the corresponding substrate, as rigid bodies which have to possess geometrically complementary regions. Indeed, proteins are not rigid and contain flexible side chains, but studies revealed that the backbone - the skeletal structure consisting of the functional groups linked by peptide bonds - only changes barely during the formation of the complex.
In general, the docking process does not return only one specific drug candidate but rather a large number of molecules which fulfill the mere physical preconditions to interact with the target. From the set of these candidates those molecules have to be chosen which are considered to be effective drugs. Possible problems can arise thereby that the designed drug for example is not able to reach the target, since it is exposed to a large variety of different environments and biological barriers.