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WIREs Syst Biol Med
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Simulation of cellular biochemical system kinetics

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Abstract The goal of realistically and reliably simulating the biochemical processes underlying cellular function is achievable through a systematic approach that makes use of the broadest possible amount of in vitro and in vivo data, and is consistent with all applicable physical chemical theories. Progress will be facilitated by establishing: (1) a concrete self‐consistent theoretical foundation for systems simulation; (2) extensive and accurate databases of thermodynamic properties of biochemical reactions; (3) parameterized and validated models of enzyme and transporter catalytic mechanisms that are consistent with physical chemical theoretical foundation; and (4) software tools for integrating all these concepts, data, and models into a cohesive representation of cellular biochemical systems. Ongoing initiatives are laying the groundwork for the broad‐based community cooperation that will be necessary to pursue these elements of a strategic infrastructure for systems simulation on a large scale. WIREs Syst Biol Med 2011 3 136–146 DOI: 10.1002/wsbm.116 This article is categorized under: Models of Systems Properties and Processes > Cellular Models

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Strategic approach to biochemical systems modeling and analysis. Models are constructed based on three major data sets: biochemical thermodynamics, kinetics of enzymes in vitro, and systems‐level data, such as from intact organelles, cells, tissues, and/or organs. Thermodynamic data are used to construct databases of thermodynamic properties; enzyme kinetic data and thermodynamic property data are used to develop models of individual enzyme and transporter mechanisms. Individual enzyme and transporter models are integrated together to build systems‐level models that are parameterized and validated using systems‐level data.

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