ArticleBioinformatics (Oxford, England)2018
Selenzyme: enzyme selection tool for pathway design.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
What it found
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Who cites it
58 citing papers in PubMed.
- Enhancing biocatalytic retrosynthesis with a graph-to-graph model.Chemical science · 2026Article
- Applications and limitations of AI tools in enzyme design.Protein science : a publication of the Protein Society · 2026Review
- 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
- How far can you go? Extrapolating values of catalytic activity from known protein landscapes in natural and directed evolution.Chemical Society reviews · 2026Review
- EnzRetro: Enzymatic Retrosynthetic Planning With Site-Specific Reaction Edits Based on Sequence Generative Architecture.Exploration (Beijing, China) · 2026Article
- Advances in Machine Learning Models for Predicting Enzyme Kinetic Parameters.Journal of chemical information and modeling · 2026Review
- A highly active Burkholderia polyketoacyl-CoA thiolase for production of triacetic acid lactone.Nature communications · 2025Article
- A virtual platform for automated hybrid organic-enzymatic synthesis planning.Nature communications · 2025Article
- Computational approaches to enzymatic reaction assignment: a review of methods, validations, and future directions.Briefings in bioinformatics · 2025Review
- Unravelling the Functional Diversity of Type III Polyketide Synthases in Fungi.Angewandte Chemie (International ed. in English) · 2025Article
- From reactants to products: computational methods for biosynthetic pathway design.Synthetic and systems biotechnology · 2025Review
- novoStoic2.0: An integrated framework for pathway synthesis, thermodynamic evaluation, and enzyme selection.PLoS computational biology · 2025Article
- 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
- CatPred: a comprehensive framework for deep learning in vitro enzyme kinetic parameters.Nature communications · 2025Article
- Engineering an Escherichia coli strain for enhanced production of flavonoids derived from pinocembrin.Microbial cell factories · 2024Article
- Artificial Intelligence Methods and Models for Retro-Biosynthesis: A Scoping Review.ACS synthetic biology · 2024Article
- Developing BioNavi for Hybrid Retrosynthesis Planning.JACS Au · 2024Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Summary: Synthetic biology applies the principles of engineering to biology in order to create biological functionalities not seen before in nature. One of the most exciting applications of synthetic biology is the design of new organisms with the ability to produce valuable chemicals including pharmaceuticals and biomaterials in a greener; sustainable fashion. Selecting the right enzymes to catalyze each reaction step in order to produce a desired target compound is, however, not trivial. Here, we present Selenzyme, a free online enzyme selection tool for metabolic pathway design. The user is guided through several decision steps in order to shortlist the best candidates for a given pathway step. The tool graphically presents key information about enzymes based on existing databases and tools such as: similarity of sequences and of catalyzed reactions; phylogenetic distance between source organism and intended host species; multiple alignment highlighting conserved regions, predicted catalytic site, and active regions and relevant properties such as predicted solubility and transmembrane regions. Selenzyme provides bespoke sequence selection for automated workflows in biofoundries. Availability and implementation: The tool is integrated as part of the pathway design stage into the design-build-test-learn SYNBIOCHEM pipeline. The Selenzyme web server is available at http://selenzyme.synbiochem.co.uk. Supplementary information: Supplementary data are available at Bioinformatics online.
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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.