Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI, USA.
Wiley Interdiscip Rev Syst Biol Med. 2011 Mar-Apr;3(2):136-46. doi: 10.1002/wsbm.116. Epub 2010 Dec 17.
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.
通过系统的方法，利用尽可能广泛的体外和体内数据，并与所有适用的物理化学理论一致，可以实现真实可靠地模拟细胞功能背后的生化过程。通过以下措施可以促进进展：（1）为系统模拟建立具体的一致的理论基础；（2）广泛而准确的生化反应热力学性质数据库；（3）与物理化学理论基础一致的酶和转运体催化机制的参数化和验证模型；（4）用于将所有这些概念、数据和模型集成到细胞生化系统的连贯表示中的软件工具。正在进行的计划为广泛的社区合作奠定了基础，这对于在大规模上追求系统模拟的战略基础设施的这些要素是必要的。
