Modeling for (physical) biologists: an introduction to the rule-based approach.
Modeling for (physical) biologists: an introduction to the rule-based approach.
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DOI：
10.1088/1478-3975/12/4/045007
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发表时间：
2015-07-16
期刊：
影响因子：
2
通讯作者：
Hlavacek WS
中科院分区：
文献类型：
--
作者：
Chylek LA;Harris LA;Faeder JR;Hlavacek WS
捕获细胞调节网络的化学动力学的模型可以根据生物分子相互作用的规则来指定。一个规则定义了一个广义反应，意思是一个允许多个反应物的反应，每个反应物都能够参与一个特征转化，并且每个反应物都具有某些特定的属性，这些属性可能是局部的，例如蛋白质的特定位点或结构域的状态。换句话说，规则定义了转换和反应物参与转换必须具备的属性。规则还提供了费率定律。基于规则的建模方法可以考虑生物分子功能位点水平上的机制细节，并为构建计算模型提供了一种方便和可视化的方法，可以分析研究系统级行为如何从组件相互作用中产生。
Models that capture the chemical kinetics of cellular regulatory networks can be specified in terms of rules for biomolecular interactions. A rule defines a generalized reaction, meaning a reaction that permits multiple reactants, each capable of participating in a characteristic transformation and each possessing certain, specified properties, which may be local, such as the state of a particular site or domain of a protein. In other words, a rule defines a transformation and the properties that reactants must possess to participate in the transformation. A rule also provides a rate law. A rule-based approach to modeling enables consideration of mechanistic details at the level of functional sites of biomolecules and provides a facile and visual means for constructing computational models, which can be analyzed to study how system-level behaviors emerge from component interactions.