ArticleNucleic acids research2024
REME: an integrated platform for reaction enzyme mining and evaluation.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Enhancing biocatalytic retrosynthesis with a graph-to-graph model.Chemical science · 2026Article
- SynBioGPT2: A dynamic reasoning framework enables high-fidelity design of microbial cell factories.Biodesign research · 2026Article
- Article
- A multi-dimensional engineering strategy integrating computational design, self-cyclization and whole cell biocatalysis for efficient epilactose production.Food chemistry: X · 2026Article
- De novo L-(+)-tartaric acid biosynthesis in multi-modular engineered yeasts.Nature communications · 2026Article
- EnzymeMiner 2.0: advancing automated enzyme discovery with expansive sequence mining and smart property analysis.Nucleic acids research · 2026Article
- CACLENS: A Multitask Deep Learning System for Enzyme Discovery.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Protein design drives synthetic biology research of plant natural products.Biodesign research · 2025Review
- Sequence and taxonomic feature evaluation facilitated the discovery of alcohol oxidases.Synthetic and systems biotechnology · 2025Article
- ActSeek: fast and accurate search algorithm of active sites in alphafold database.Bioinformatics (Oxford, England) · 2025Article
- DeepMolecules: a web server for predicting enzyme and transporter-small molecule interactions.Nucleic acids research · 2025Article
- Review
- DEKP: a deep learning model for enzyme kinetic parameter prediction based on pretrained models and graph neural networks.Briefings in bioinformatics · 2025Article
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Authors and funding
13 authors.
Funding
Abstract
A key challenge in pathway design is finding proper enzymes that can be engineered to catalyze a non-natural reaction. Although existing tools can identify potential enzymes based on similar reactions, these tools encounter several issues. Firstly, the calculated similar reactions may not even have the same reaction type. Secondly, the associated enzymes are often numerous and identifying the most promising candidate enzymes is difficult due to the lack of data for evaluation. Thirdly, existing web tools do not provide interactive functions that enable users to fine-tune results based on their expertise. Here, we present REME (https://reme.biodesign.ac.cn/), the first integrated web platform for reaction enzyme mining and evaluation. Combining atom-to-atom mapping, atom type change identification, and reaction similarity calculation enables quick ranking and visualization of reactions similar to an objective non-natural reaction. Additional functionality enables users to filter similar reactions by their specified functional groups and candidate enzymes can be further filtered (e.g. by organisms) or expanded by Enzyme Commission number (EC) or sequence homology. Afterward, enzyme attributes (such as kcat, Km, optimal temperature and pH) can be assessed with deep learning-based methods, facilitating the swift identification of potential enzymes that can catalyze the non-natural reaction.
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Registered trials
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