Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems.
Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems.
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基于规则的建模：一种用于研究细胞信号系统中生物分子位点动态的计算方法。
DOI：
10.1002/wsbm.1245
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发表时间：
2014-01
影响因子：
7.9
通讯作者：
Hlavacek, William S.
中科院分区：
文献类型：
--
作者：
Chylek, Lily A.;Harris, Leonard A.;Tung, Chang-Shung;Faeder, James R.;Lopez, Carlos F.;Hlavacek, William S.
基于规则的建模是为了解决细胞信号系统中化学动力学建模的传统方法的局限性而开发的。这些系统由多个相互作用的生物分子（如蛋白质）组成，这些生物分子本身由多个部分（如结构域、线性基序和磷酸化位点）组成。因此，介导信息处理的生物分子通常具有以多种方式相互作用的潜力，随着二元相互作用的考虑，可能的复合物和翻译后修饰状态的数量趋于指数增长。因此，只有大型反应网络才能捕获细胞信号系统中发生的分子相互作用的所有可能后果，这是有问题的，因为化学动力学的传统建模方法（例如，常微分方程）需要明确的网络规范。这个问题可以通过用局部规则表示交互来规避。使用这种方法，网络规范是隐式的，模型规范是简洁的。简明的表示导致化学动力学的粗粒化，这是因为一个规则所隐含的所有反应都继承与该规则相关的速率定律。如果交互是模块化的，那么粗粒度是合适的，并且模型的粗粒度可以根据需要进行调整。可以使用专门的模型规范语言来指定规则，并且最近开发的用于规范基于规则的模型的工具允许利用强大的软件工程功能。基于规则的模型由一组规则组成，这些规则可以通过通用模拟和分析工具进行处理，以实现不同的目标（例如，执行确定性或随机模拟）。
Rule-based modeling was developed to address the limitations of traditional approaches for modeling chemical kinetics in cell signaling systems. These systems consist of multiple interacting biomolecules (e.g., proteins), which themselves consist of multiple parts (e.g., domains, linear motifs, and sites of phosphorylation). Consequently, biomolecules that mediate information processing generally have the potential to interact in multiple ways, with the number of possible complexes and post-translational modification states tending to grow exponentially with the number of binary interactions considered. As a result, only large reaction networks capture all possible consequences of the molecular interactions that occur in a cell signaling system, which is problematic because traditional modeling approaches for chemical kinetics (e.g., ordinary differential equations) require explicit network specification. This problem is circumvented through representation of interactions in terms of local rules. With this approach, network specification is implicit and model specification is concise. Concise representation results in a coarse graining of chemical kinetics, which is introduced because all reactions implied by a rule inherit the rate law associated with that rule. Coarse graining can be appropriate if interactions are modular, and the coarseness of a model can be adjusted as needed. Rules can be specified using specialized model-specification languages, and recently developed tools designed for specification of rule-based models allow one to leverage powerful software engineering capabilities. A rule-based model comprises a set of rules, which can be processed by general-purpose simulation and analysis tools to achieve different objectives (e.g., to perform either a deterministic or stochastic simulation).
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影响因子：
5.8
作者：
Bornstein, Benjamin J.;Keating, Sarah M.;Hucka, Michael
通讯作者：
Hucka, Michael
影响因子：
48
作者：
Angermann, Bastian R.;Klauschen, Frederick;Meier-Schellersheim, Martin
通讯作者：
Meier-Schellersheim, Martin
影响因子：
9.9
作者：
Chen, William W.;Schoeberl, Birgit;Jasper, Paul J.;Niepel, Mario;Nielsen, Ulrik B.;Lauffenburger, Douglas A.;Sorger, Peter K.
通讯作者：
Sorger, Peter K.
DOI：
10.1007/978-1-61779-361-5_26
发表时间：
2012-01-01
期刊：
BACTERIAL MOLECULAR NETWORKS: METHODS AND PROTOCOLS
影响因子：
--
作者：
Andrews, Steven S.
通讯作者：
Andrews, Steven S.
影响因子：
2.3
作者：
Borisov NM;Chistopolsky AS;Faeder JR;Kholodenko BN
通讯作者：
Kholodenko BN