Difference between revisions of "Team:TU-Eindhoven/Model/2D Simulation"

Revision as of 17:02, 20 October 2017

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Simulation in 2D

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.
In the legend you can see how the three different parts are visualized during the simulation. If a complex is formed, the Binding Partners should bind to the Protein Scaffold at the same orientation. An example of a complex can be seen in Figure 2.
Before the simulation is executed, some parameters need to be defined.

Size of the simulation box

Number of steps in the simulation

Temperature

Valence

Of the Scaffold Construct

Of the Binding Construct

Length of the Linker (maximum distance between parts of the same construct)

Of the Scaffold Construct

Of the Binding Construct

Amount of Constructs

Of the Scaffold

Of the Binding Partner

Interactions between the parts

With the solvent

If the parts can form a complex

If scaffold and binding parts are next to each other and have the right orientation for complex formation, but are not at the correct position

If scaffold and binding parts are next to each other and don’t have the right orientation for complex formation

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