In the simulation three different constructs are present (Figure 1), which can move and rotate in accordance with a Monte Carlo algorithm. The first construct, the Scaffold Construct, consists of the parts of the Protein Scaffold were the inducer is already bound. The parts of the same construct can move separately, but with some restriction. The restrictions include the limitation of the distance between the parts and that the movement should be energetically possible. The other two parts (Center Point and Binding Partner) are connected and form the Binding Construct. There is a Center Point and at this Center Point, four Binding Partner parts can bind. The Binding Partners are also flexibly connected to the Center Point part, with the same restrictions as mentioned before.
