Moleculizer is a tool for simulating and generating biochemical reaction networks that are specified through a set of rules for protein-protein interactions.It was designed to enable a researcher to simulate the behavior of intracellular signaling systems over time and in response to defined perturbations. The outcomes of the simulations can then be tested experimentally. A unique feature of Moleculizer is that it generates species and reactions, as they are needed. This ‘on- the-fly’ mode saves time by increasing computational speed and reducing manual input by the researcher. Moleculizer uses Monte Carlo methods to simulate the reactions. Moleculizer models can be exported as SBML files that can be subsequently imported into other modeling and simulation software such as ECell.
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Moleculizer is available to the public under the Lesser GNU Public License.
Lok, L and Brent, R. Automatic generation of cellular reaction networks with Moleculizer 1.0. Nature Biotechnology, 1:131-136 (2005).