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.