This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Biochemical network modeling of multi-component complexes results in a combinatorial explosion of distinct molecular states (each with a particular combination of binding sites filled) and state transitions (reactions). The underlying mechanistic description, however, can often be summarized in a compact form, a description of individual interactions only enough context to quantify those dependent bindings. This compact form can be formalized as a set of elementary molecules with named binding sites (or domains) and a set of reaction rules. In collaboration with Michael Blinov of Los Alamos National Laboratory, we are investigating the integration of his BioNetGen rules-based biochemical network generator into the Virtual Cell framework. We are pursing separate funding to fully integrate the existing BioNetGen capabilities within the conceptual framework of the Virtual Cell, and to start collaborative research in other aspects of managing combinatorial complexity.
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