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Bioinformatics Advance Access originally published online on June 24, 2004
Bioinformatics 2004 20(17):3289-3291; doi:10.1093/bioinformatics/bth378
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Bioinformatics vol. 20 issue 17 © Oxford University Press 2004; all rights reserved.

Applications Note

BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains

Michael L. Blinov , James R. Faeder , Byron Goldstein and William S. Hlavacek *

Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA

Received on May 17, 2004; revised on June 8, 2004; accepted on June 19, 2004
Advance Access Publication June 24, 2004

Summary: BioNetGen allows a user to create a computational model that characterizes the dynamics of a signal transduction system, and that accounts comprehensively and precisely for specified enzymatic activities, potential post-translational modifications and interactions of the domains of signaling molecules. The output defines and parameterizes the network of molecular species that can arise during signaling and provides functions that relate model variables to experimental readouts of interest. Models that can be generated are relevant for rational drug discovery, analysis of proteomic data and mechanistic studies of signal transduction.

Availability: http://cellsignaling.lanl.gov/bionetgen

Contact: bionetgen{at}lanl.gov

* To whom correspondence should be addressed.


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