To predict the designed system, iGEM TU Eindhoven developed a model to simulate the designed protein scaffold and its binding partner. The challenge is that there are many options of end products, making it impossible to apply an ordinary ODE-solver with differential equations. There are two approaches that we will introduce. The first is a simulation that we developed ourselves and that visualizes the system in a 2D simulation box.The second approach uses an already developed rule-based-model, which we adapted to our system.
To get a more detailed description, go to the model page of “Simulation in 2D” and “Rule based model”, or continue with reading to get a short overview of the molecules that are simulated with the models.
