ArticleComputational and structural biotechnology journal2023
SelenzymeRF: updated enzyme suggestion software for unbalanced biochemical reactions.
Article in Computational and structural biotechnology journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed.
- Applications and limitations of AI tools in enzyme design.Protein science : a publication of the Protein Society · 2026Review
- Bridging Algorithms and Biocatalysis: Perspectives on AI-Supported Enzyme Engineering.Molecules (Basel, Switzerland) · 2026Review
- A virtual platform for automated hybrid organic-enzymatic synthesis planning.Nature communications · 2025Article
- Before LUCA: unearthing the chemical roots of metabolism.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- From reactants to products: computational methods for biosynthetic pathway design.Synthetic and systems biotechnology · 2025Review
- RC-GNN: A predictive model of enzyme-reaction pairs.bioRxiv : the preprint server for biology · 2025Article
- Synthetic Biology of Natural Products Engineering: Recent Advances Across the Discover-Design-Build-Test-Learn Cycle.ACS synthetic biology · 2024Review
- Artificial Intelligence Methods and Models for Retro-Biosynthesis: A Scoping Review.ACS synthetic biology · 2024Article
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4 authors.
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Abstract
Selenzyme is a retrobiosynthesis tool that suggests candidate enzymes for user query reactions. Enzyme suggestions are based on identical reactions, as well as similar reactions, since enzymes are often capable of promiscuous substrate binding. Selenzyme is a user-friendly, widely used web-tool for ranking enzymes based on reaction similarity and additional features, including the phylogenetic distance between the source species of the enzyme and the intended host. While Selenzyme has proved invaluable in assisting with enzyme selection for known reactions, as well as many novel or orphan reactions, weaknesses have been exposed in its ability to rank functionally related enzymes. Within this update, we introduce a new reaction similarity scoring algorithm, which is used in conjunction with the previous similarity calculation, to improve the accuracy of enzyme suggestions based on non-identical similar reactions, across a range of EC reaction classes. This allows enzymes to be suggested for reactions not found within the database, even if the reaction is unbalanced. A database update was also carried out, to ensure that reaction and enzyme knowledge remains current. This update can be accessed at http://selenzymeRF.synbiochem.co.uk/.
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