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首页> 外文期刊>Briefings in bioinformatics >Computational resources and strategies to construct single-molecule metabolic models of microbial cells
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Computational resources and strategies to construct single-molecule metabolic models of microbial cells

机译：构建微生物细胞单分子代谢模型的计算资源和策略

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Recent computational methodologies, such as individual-based modelling, pave the way to the search for explanatory insight into the collective behaviour of molecules. Many reviews offer an up-to-date perspective about such methodologies, but little is discussed about the practical information requirements involved. The biological information used as input should be easily and routinely determined in the laboratory, publicly available and, preferably, organized in programmatically accessible databases. This review is the first to provide a systematic and comprehensive overview of available resources for the modelling of metabolic events at the molecular scale. The glycolysis pathway of Escherichia coli, which is one of the most studied pathways in Microbiology, serves as case study. This curation addressed structural information about E. coli (i.e. defining the simulation environment), the reactions forming the glycolysis pathway including the enzymes and the metabolites (i.e. the molecules to be represented), the kinetics of each reaction (i.e. behavioural logic of the molecules) and diffusion parameters for all enzymes and metabolites (i.e. molecule movement in the environment). Furthermore, the interpretation of relevant biological features, such as molecular diffusion and enzyme kinetics, and the connection of experimental determination and simulation validation are detailed. Notably, the information from classical theories, such as enzymatic rates and diffusion coefficients, is translated to simulation parameters, such as collision efficiency and particle velocity.
机译：最近的计算方法，例如基于个体的建模，为寻求对分子集体行为的解释性见解铺平了道路。许多评论提供了有关此类方法的最新观点，但很少涉及所涉及的实际信息要求。用作输入的生物学信息应在实验室中容易且常规地确定，可公开获得，最好在程序可访问的数据库中进行组织。这篇综述是第一个提供系统和全面的概述可利用资源的分子水平代谢事件建模的综述。大肠杆菌的糖酵解途径是微生物学中研究最多的途径之一，是案例研究。该策展内容涉及大肠杆菌的结构信息（即定义模拟环境），形成糖酵解途径的反应（包括酶和代谢物）（即要表示的分子），每个反应的动力学（即分子的行为逻辑） ）和所有酶和代谢物的扩散参数（即分子在环境中的移动）。此外，详细解释了相关生物学特征，例如分子扩散和酶动力学，以及实验测定和模拟验证之间的联系。值得注意的是，来自经典理论的信息（例如酶速率和扩散系数）被转换为模拟参数（例如碰撞效率和粒子速度）。

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