Synthetic biology and metabolic engineering rely on computational search tools for predictions of novel biosynthetic pathways to industrially important compounds, many of which are derived from aromatic amino acids. Pathway search tools vary in their scope of covered reactions and compounds, as well as in metrics for ranking and evaluation. In this work, we present a new computational resource called ARBRE: Aromatic compounds RetroBiosynthesis Repository and Explorer. It consists 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 into 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. In line with the standards of open science, we have made the toolbox freely available to the scientific community on git (https://github.com/EPFL-LCSB/ARBRE) and we provide the web-version at http://lcsb-databases.epfl.ch/arbre/. We envision that ARBRE will provide the community with a new computational resource and comprehensive search tool to predict and rank pathways towards industrially important aromatic compounds.

合成生物学和代谢工程依赖计算搜索工具来预测工业上重要化合物的新生物合成途径，其中许多化合物来源于芳香族氨基酸。通路搜索工具在涵盖的反应和化合物范围以及排名和评估指标方面各不相同。在这项工作中，我们提出了一种名为 ARBRE 的新计算资源：芳香族化合物 RetroBiosynthesis Repository 和 Explorer。它由一个以芳香族氨基酸生物合成为中心的综合生化反应网络和一个用于导航该网络的计算工具箱组成。ARBRE 包含超过 33,000 种已知反应和 390,000 种新反应，通过广义酶促反应规则和超过 74,000 种化合物进行预测，其中 19'000 为生化数据库所知，55'000 只为 PubChem 所知。超过 1,000 个分子以前只是 PubChem 数据库的一部分，以前不可能整合到生化网络中，这些分子通过指定酶促反应被包含到 ARBRE 反应网络中。ARBRE 可用于围绕已知生化途径和木质素降解产物的途径搜索、酶注释、途径排序、可视化和网络扩展，以预测有价值的化合物衍生。根据开放科学的标准，我们在 git (https://github.com/EPFL-LCSB/ARBRE) 上向科学界免费提供了该工具箱，我们在 http://lcsb 提供了网络版本-databases.epfl.ch/arbre/。