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Open Access Methodology article

Exact model reduction of combinatorial reaction networks

Holger Conzelmann1*, Dirk Fey2 and Ernst D Gilles1

Author Affiliations

1 Max-Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany

2 Industrial Control Centre, Department of Electronic & Electrical Engineering, University of Strathclyde, Glasgow, Scotland, UK

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BMC Systems Biology 2008, 2:78  doi:10.1186/1752-0509-2-78

Published: 28 August 2008

Abstract

Background

Receptors and scaffold proteins usually possess a high number of distinct binding domains inducing the formation of large multiprotein signaling complexes. Due to combinatorial reasons the number of distinguishable species grows exponentially with the number of binding domains and can easily reach several millions. Even by including only a limited number of components and binding domains the resulting models are very large and hardly manageable. A novel model reduction technique allows the significant reduction and modularization of these models.

Results

We introduce methods that extend and complete the already introduced approach. For instance, we provide techniques to handle the formation of multi-scaffold complexes as well as receptor dimerization. Furthermore, we discuss a new modeling approach that allows the direct generation of exactly reduced model structures. The developed methods are used to reduce a model of EGF and insulin receptor crosstalk comprising 5,182 ordinary differential equations (ODEs) to a model with 87 ODEs.

Conclusion

The methods, presented in this contribution, significantly enhance the available methods to exactly reduce models of combinatorial reaction networks.