Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks
Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks
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DOI：
10.1089/cmb.2008.0044
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发表时间：
2008-07-01
影响因子：
1.7
通讯作者：
Kohlbacher, Oliver
中科院分区：
文献类型：
--
作者：
Blum, Torsten;Kohlbacher, Oliver
代谢网络路径的计算分析在系统生物学中有许多应用。虽然已经提出了基于图论的方法来寻找这些网络中从一种代谢物到另一种代谢物的生物转化路线，但这些方法大多数都发现了太多的路线，其中大多数在生物学上不可行或毫无意义。我们提出了一种基于原子映射规则（描述化学反应中哪些离析物原子映射到哪些产物原子）寻找相关路线的新方法。这导致问题被重新表述为度加权代谢网络中的最轻路径搜索。该方法的关键组成部分是计算最佳原子映射规则的新方法。
Computational analysis of pathways in metabolic networks has numerous applications in systems biology. While graph theory-based approaches have been presented that find biotransformation routes from one metabolite to another in these networks, most of these approaches suffer from finding too many routes, most of which are biologically infeasible or meaningless. We present a novel approach for finding relevant routes based on atom mapping rules (describing which educt atoms are mapped onto which product atoms in a chemical reaction). This leads to a reformulation of the problem as a lightest path search in a degree-weighted metabolic network. The key component of the approach is a new method of computing optimal atom mapping rules.