Working group: "Computational Biology"

2010, the 09th of March

Jérôme Feret

Title: Internal coarse-graining of molecular systems


Modelers of molecular signaling networks must cope with the combinatorial explosion of protein states generated by post-translational modifications and complex formation. Rule-based models provide a powerful alternative to approaches that require an explicit enumeration of all possible molecular species of a system. Such models consist of formal rules stipulating the (partial) contexts for specific protein-protein interactions to occur. These contexts specify molecular patterns that are usually less detailed than molecular species. Yet, the execution of rule-based dynamics requires stochastic simulation, which can be very costly. It thus appears desirable to convert a rule-based model into a reduced system of differential equations by exploiting the lower resolution at which rules specify interactions.