Internal coarse-graining of molecular systems.

ABSTRACT: Modelers of molecular signaling networks must cope with the combinatorial explosion of protein states generated by posttranslational modifications and complex formation. Rule-based models provide a powerful alternative to approaches that require explicit enumeration of all possible molecular species of a system. Such models consist of formal rules stipulating the (partial) contexts wherein specific protein-protein interactions 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 granularity at which rules specify interact

SUBMITTER: Feret J 

PROVIDER: S-EPMC2672529 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature