Supplementary datasets for "ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds"

Supplementary datasets accompanying the manuscript "ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds" published in the Metabolic Engineering Journal (https://doi.org/10.1016/j.ymben.2022.03.013). In line with the standards of open science, the ARBRE toolbox is freely available to the scientific community on gitHub (https://github.com/EPFL-LCSB/ARBRE) and we also provide the web-version at http://lcsb-databases.epfl.ch/arbre/

ARBRE: Aromatic compounds RetroBiosynthesis Repository and Explorer is a new computational resource consisting of a comprehensive biochemical reaction network centered around aromatic amino acid biosynthesis and a computational toolbox for navigating this network. ARBRE encompasses over 33′000 known and 390′000 novel reactions predicted with generalized enzymatic reactions rules and over 74′000 compounds, of which 19′000 are known to biochemical databases and 55′000 only to PubChem. Over 1′000 molecules that were solely part of the PubChem database before and were previously impossible to integrate into a biochemical network are included in the ARBRE reaction network by assigning enzymatic reactions. ARBRE can be applied for pathway search, enzyme annotation, pathway ranking, visualization, and network expansion around known biochemical pathways and products of lignin degradation to predict valuable compound derivations.

Supplementary files are organized as follows:

- 1-s2.0-S1096717622000490-mmc4.docx contains Supplementary Figures 1-4 and Tables 1, 2,  and 4.

- 1-s2.0-S1096717622000490-mmc2.xlsx contains Supplementary Table 3.

- 1-s2.0-S1096717622000490-mmc1.xlsx contains Supplementary Table 5

- 1-s2.0-S1096717622000490-mmc3.xlsx contains Supplementary Table 6

本数据集为发表于《代谢工程期刊》（Metabolic Engineering Journal，https://doi.org/10.1016/j.ymben.2022.03.013）的论文《ARBRE：预测工业重要芳香族化合物合成途径的计算资源》的配套补充数据集。遵循开放科学标准，ARBRE工具箱已在GitHub（https://github.com/EPFL-LCSB/ARBRE）上向科研社群免费开放，同时我们还提供了其网页版，网址为http://lcsb-databases.epfl.ch/arbre/。

ARBRE（Aromatic compounds RetroBiosynthesis Repository and Explorer，芳香族化合物逆向生物合成库与探索器）是一款全新计算资源，由以芳香族氨基酸生物合成为核心的全覆盖生化反应网络，以及用于遍历该网络的计算工具箱共同构成。ARBRE涵盖超过33000条已知反应与390000条基于通用酶促反应规则预测得到的全新反应，同时收录超过74000种化合物，其中19000种可在现有生化数据库中查询到，剩余55000种仅收录于PubChem数据库。此前仅收录于PubChem数据库且无法被整合进生化网络的1000余种分子，如今通过关联酶促反应被纳入ARBRE的反应网络中。ARBRE可用于途径搜索、酶注释、途径排序、可视化操作，以及围绕已知生化途径与木质素降解产物开展网络扩展，以预测高价值化合物的衍生路径。

补充文件的组织形式如下：
- 1-s2.0-S1096717622000490-mmc4.docx 包含补充图1至补充图4，以及补充表1、补充表2与补充表4。
- 1-s2.0-S1096717622000490-mmc2.xlsx 包含补充表3。
- 1-s2.0-S1096717622000490-mmc1.xlsx 包含补充表5。
- 1-s2.0-S1096717622000490-mmc3.xlsx 包含补充表6。