ArticleNucleic acids research2019
RetroRules: a database of reaction rules for engineering biology.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Mechanism-informed rules tunably balance novelty and feasibility of predicted enzymatic reactions.bioRxiv : the preprint server for biology · 2026Article
- Discover the maze-like network for glabridin biosynthesis.Nature communications · 2026Article
- RetroRules 2026: an expanded database combining biochemical and organic reaction templates for pathway discovery.Nucleic acids research · 2026Article
- The consolidation of open-source computer-assisted chemical synthesis data into a comprehensive database.Journal of cheminformatics · 2025Article
- Before LUCA: unearthing the chemical roots of metabolism.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Computational tools for nonnatural pathway design: Algorithms, applications, and challenges.Biodesign research · 2025Review
- Graph-sequence enhanced transformer for template-free prediction of natural product biosynthesis.Patterns (New York, N.Y.) · 2025Article
- Measuring catalytic mechanism similarity - a new approach to study enzyme function and evolution.The FEBS journal · 2025Article
- Merging the computational design of chimeric type I polyketide synthases with enzymatic pathways for chemical biosynthesis.Nature communications · 2025Article
- MEANtools integrates multi-omics data to identify metabolites and predict biosynthetic pathways.PLoS biology · 2025Article
- RC-GNN: A predictive model of enzyme-reaction pairs.bioRxiv : the preprint server for biology · 2025Article
- High-resolution multiomics links nutrients and mixotrophy to toxicity in a harmful bloom of the haptophyteScience advances · 2025Article
- MicrobeRX: a tool for enzymatic-reaction-based metabolite prediction in the gut microbiome.Microbiome · 2025Article
- Molecular Structure Discovery for Untargeted Metabolomics Using Biotransformation Rules and Global Molecular Networking.Analytical chemistry · 2025Article
- Computational analysis of the gut microbiota-mediated drug metabolism.Computational and structural biotechnology journal · 2025Article
- Deep learning in template-free de novo biosynthetic pathway design of natural products.Briefings in bioinformatics · 2024Review
- Artificial Intelligence Methods and Models for Retro-Biosynthesis: A Scoping Review.ACS synthetic biology · 2024Article
- DetSpace: a web server for engineering detectable pathways for bio-based chemical production.Nucleic acids research · 2024Article
- Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota.NPJ systems biology and applications · 2024Article
- EnzymeMap: curation, validation and data-driven prediction of enzymatic reactions.Chemical science · 2023Article
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Authors and funding
4 authors.
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Abstract
RetroRules is a database of reaction rules for metabolic engineering (https://retrorules.org). Reaction rules are generic descriptions of chemical reactions that can be used in retrosynthesis workflows in order to enumerate all possible biosynthetic routes connecting a target molecule to its precursors. The use of such rules is becoming increasingly important in the context of synthetic biology applied to de novo pathway discovery and in systems biology to discover underground metabolism due to enzyme promiscuity. Here, we provide for the first time a complete set containing >400 000 stereochemistry-aware reaction rules extracted from public databases and expressed in the community-standard SMARTS (SMIRKS) format, augmented by a rule representation at different levels of specificity (the atomic environment around the reaction center). Such numerous representations of reactions expand natural chemical diversity by predicting de novo reactions of promiscuous enzymes.
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Registered trials
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