ArticleChemical science2023
EnzymeMap: curation, validation and data-driven prediction of enzymatic reactions.
Article in Chemical science, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed, 33 citations in OpenAlex.
- Pockets to products: a data-driven approach for classification of monoterpene synthases.Digital discovery · 2026Article
- Enhancing biocatalytic retrosynthesis with a graph-to-graph model.Chemical science · 2026Article
- TridentSynth: a webtool for the retrosynthesis of molecules using chimeric type I polyketide synthases and chemoenzymatic pathways.Nucleic acids research · 2026Article
- CBR-db: A Cheminformatic Database for Biochemical Reaction Analysis.ACS synthetic biology · 2026Article
- Predicting enzyme-compound associations for enzyme-catalysed reactions.Journal of cheminformatics · 2026Article
- SynRXN: An Open Benchmark and Curated Dataset for Computational Reaction Modeling.Scientific data · 2026Article
- Dual-encoder contrastive learning accelerates enzyme discovery.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Nature-Inspired Enzymatic Cascades: Emerging Strategies for Sustainable Chemistry.Molecules (Basel, Switzerland) · 2026Review
- AI-Driven Enzyme Engineering: Emerging Models and Next-Generation Biotechnological Applications.Molecules (Basel, Switzerland) · 2025Review
- Computational approaches to enzymatic reaction assignment: a review of methods, validations, and future directions.Briefings in bioinformatics · 2025Review
- Computational tools for nonnatural pathway design: Algorithms, applications, and challenges.Biodesign research · 2025Review
- Merging the computational design of chimeric type I polyketide synthases with enzymatic pathways for chemical biosynthesis.Nature communications · 2025Article
- RC-GNN: A predictive model of enzyme-reaction pairs.bioRxiv : the preprint server for biology · 2025Article
- Review
- The transcriptomic footprint of Mytella strigata: de novo transcriptome assembly of a major invasive species.Scientific data · 2025Article
- De novo transcriptome assembly of the Perna viridis: A novel invertebrate model for ecotoxicological studies.Scientific data · 2025Article
- Self-supervised domain adaptation of protein language model based solely on positive enzyme-reaction pairs.Computational and structural biotechnology journal · 2025Article
- PhenoMultiOmics: an enzymatic reaction inferred multi-omics network visualization web server.Bioinformatics (Oxford, England) · 2024Article
- Artificial Intelligence Methods and Models for Retro-Biosynthesis: A Scoping Review.ACS synthetic biology · 2024Article
- REME: an integrated platform for reaction enzyme mining and evaluation.Nucleic acids research · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Enzymatic reactions are an ecofriendly, selective, and versatile addition, sometimes even alternative to organic reactions for the synthesis of chemical compounds such as pharmaceuticals or fine chemicals. To identify suitable reactions, computational models to predict the activity of enzymes on non-native substrates, to perform retrosynthetic pathway searches, or to predict the outcomes of reactions including regio- and stereoselectivity are becoming increasingly important. However, current approaches are substantially hindered by the limited amount of available data, especially if balanced and atom mapped reactions are needed and if the models feature machine learning components. We therefore constructed a high-quality dataset (EnzymeMap) by developing a large set of correction and validation algorithms for recorded reactions in the literature and showcase its significant positive impact on machine learning models of retrosynthesis, forward prediction, and regioselectivity prediction, outperforming previous approaches by a large margin. Our dataset allows for deep learning models of enzymatic reactions with unprecedented accuracy, and is freely available online.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.