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Updated: Jan 31, 2026

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从KEGG RCLASS数据中计算双推出图形转换规则和原子对原子映射

Nora Beier¹, Thomas Gatter¹, Jakob L Andersen²

¹Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany.

Algorithms for molecular biology : AMB

|January 30, 2026

概括

新的laveau软件从KEGG RCLASS数据生成明确的DPO规则和原子对原子地图,使代谢网络的详细原子级模型成为可能.

科学领域:

生物信息学是一种生物信息学.
计算化学计算化学
系统生物学系统生物学

背景情况:

原子对原子地图对于许多应用至关重要,但很难获得.
凯格反应数据库使用RCLASSes,而不是直接的原子对原子地图,阻碍了规则构建.
DPO图形转换规则为原子级映射提供了有效的表示.

研究的目的:

开发一种将KEGG RCLASS数据转换为DPO规则的方法.
从现有的KEGG反应数据中生成明确的原子对原子地图.

主要方法:

开发了"laveau",一种工具,可以从KEGG反应和RCLASS数据中计算DPO规则.
算法将RDM代码转换为RDM模式图,根据嵌入方式将它们合并,并形成反应物/产物子图.
原子对原子地图是从RDM代码中衍生出来的,用于定义DPO转换规则.

主要成果:

从3195个RCLASSes中,laveau成功生成了1232个DPO规则和1594个原子对原子地图.
对反应物应用的生成DPO规则产生了完整的原子对原子地图.
该工具有效地从RCLASS数据中重建原子级细节.

结论:

laveau软件从KEGG RCLASSes中提取了酶催化反应的局部原子对原子地图.
为原子级代谢网络模型提供DPO规则,解决数据缺口.
促进了生物化学转换在原子水平的详细分析.

关键词:

原子对原子的映射绘制.双重推出规则双重推出规则图形重建的图形重建图形转换的图形转换方式凯格 (KEGG) 是一个代谢反应是代谢反应.这是一个RCLASS.反应规则反应规则

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