生物信息学
计算生物学
水准点(测量)
酿酒酵母
代谢工程
通量平衡分析
生物
约束(计算机辅助设计)
计算机科学
生物化学
酶
数学
基因
地理
几何学
大地测量学
作者
Mahdis Habibpour,Zahra Razaghi‐Moghadam,Zoran Nikoloski
标识
DOI:10.1016/j.ymben.2024.02.008
摘要
Metabolites, as small molecules, can act not only as substrates to enzymes, but also as effectors of activity of proteins with different functions, thereby affecting various cellular processes. While several experimental techniques have started to catalogue the metabolite-protein interactions (MPIs) present in different cellular contexts, characterizing the functional relevance of MPIs remains a challenging problem. Computational approaches from the constrained-based modeling framework allow for predicting MPIs and integrating their effects in the in silico analysis of metabolic and physiological phenotypes, like cell growth. Here, we provide a classification of all existing constraint-based approaches that predict and integrate MPIs using genome-scale metabolic networks as input. In addition, we benchmark the performance of the approaches to predict MPIs in a comparative study using different features extracted from the model structure and predicted metabolic phenotypes with the state-of-the-art metabolic networks of Escherichia coli and Saccharomyces cerevisiae. Lastly, we provide an outlook for future, feasible directions to expand the consideration of MPIs in constraint-based modeling approaches with wide biotechnological applications.
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