ANC (Allosteric Network Compiler) is a rule-based modelling tool for biochemical networks that comprise allosteric proteins. Such networks include, for example, signal transduction pathways and gene regulatory pathways. Using ANC, one can model the structure of allosteric proteins at a level of detail that accounts for their functional properties. Simple components are used as lego-like building blocks for more complex allosteric structures. You can delineate subunits and domains, binding and phosphorylation sites, and can model regulatory linkages between subunits and components. Modelling is both modular and hierarchical and so simple structures can used to construct larger, more complex structures. The figure below gives an overview of how models are created and simulated with ANC.
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PLoS Comput Biol. 2010 Nov 4;6(11):e1000975. doi: 10.1371/journal.pcbi.1000975.
Scalable rule-based modelling of allosteric proteins and biochemical networks.
Ollivier JF1, Shahrezaei V, Swain PS.