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New approaches to modeling complex biochemistry

Nature Methods volume 8, pages 130–131 (2011)Cite this article

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Combining rule-based descriptions of biochemical reactions with agent-based computer simulation opens new avenues for exploring complex cellular processes.

A major challenge in modeling complex genetic and biochemical circuits is turning imprecise 'word models' (text and drawings) into precise mathematical statements suitable for computational analysis. Many biochemical processes common to eukaryotic signaling networks are remarkably difficult to describe and simulate with rigor and precision. Assembly of multiprotein complexes or multisite post-translational modification can create a very large number of distinct molecular species from interactions involving only a handful of gene products. Such 'combinatorial complexity' exceeds the ability of conventional modeling methods to enumerate species and track their dynamics, leading to ad hoc assumptions about which types of interactions matter and which do not.

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Figure 1: Modeling the assembly of a three-protein complex, ABC, using a rule-based approach.

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  1. peter_sorger@hms.harvard.edu

Authors and Affiliations

  1. John A. Bachman and Peter Sorger are in the Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,

    John A Bachman & Peter Sorger

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  1. John A Bachman
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  2. Peter Sorger
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Bachman, J., Sorger, P. New approaches to modeling complex biochemistry. Nat Methods 8, 130–131 (2011). https://doi.org/10.1038/nmeth0211-130

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