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Carsten Maus (2008)

Component-based Modelling of RNA Structure Folding

In: Computational Methods in Systems Biology, International Conference, CMSB 2008, Rostock, Germany, October 12-15, 2008, Proceedings, vol. 5307, pp. 44-62, Berlin/Heidelberg, Springer. Lecture Notes in Computer Science.

RNA structure is fundamentally important for many biological processes. In the past decades, diverse structure prediction algorithms and tools were developed but due to missing descriptions in clearly defined modelling formalisms it’s difficult or even impossible to integrate them into larger system models. We present an RNA secondary structure folding model described in ml-Devs, a variant of the Devs formalism, which enables the hierarchical combination with other model components like RNA binding proteins. An example of transcriptional attenuation will be given where model components of RNA polymerase, the folding RNA molecule, and the translating ribosome play together in a composed dynamic model.

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