A model and analysis of the AKAP scaffold

Andrei, O. and Calder, M. (2010) A model and analysis of the AKAP scaffold. Electronic Notes in Theoretical Computer Science, 268, pp. 3-15. (doi: 10.1016/j.entcs.2010.12.002)

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We study the biochemical processes involved in scaffold-mediated crosstalk between the cAMP and the Raf-1/MEK/ERK pathways. We model the system by a continuous time Markov chain with levels and analyse properties using Continuous Stochastic Logic and the symbolic probabilistic model checker PRISM. We consider two kinds of properties of the model, causal events and pulsating behaviour, and, in order to formulate these properties, we enrich the model with trend formulas. The system is currently under wet-lab investigation and our approach was developed in collaboration with the experimentalists.

Item Type:Articles
Additional Information:Presented at CS2Bio'10 1st International Workshop on Interactions between Computer Science and Biology
Keywords:scaffold proteins, CTMC with levels, stochastic model checking, trend variables
Glasgow Author(s) Enlighten ID:Andrei, Dr Oana and Calder, Professor Muffy
Authors: Andrei, O., and Calder, M.
College/School:College of Science and Engineering > School of Computing Science
Journal Name:Electronic Notes in Theoretical Computer Science
ISSN (Online):1571-0661

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
441081SIGNAL - stochastic process algebra for biochemical signalling pathway analysisMuffy CalderEngineering & Physical Sciences Research Council (EPSRC)EP/E028519/1Computing Science