ReviewThe Biochemical journal2023
Enzyme function and evolution through the lens of bioinformatics.
Review in The Biochemical journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Methods for the establishment of enzymatic mechanisms - from QM to ML.Chemical science · 2026Review
- 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
- How far can you go? Extrapolating values of catalytic activity from known protein landscapes in natural and directed evolution.Chemical Society reviews · 2026Review
- Special Issue "Mechanism of Enzyme Catalysis: When Structure Meets Function".International journal of molecular sciences · 2026Article
- CACLENS: A Multitask Deep Learning System for Enzyme Discovery.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Computational approaches to druggable site identification: Current status and future perspective.Acta pharmaceutica Sinica. B · 2026Review
- The Ensemble Basis of Allostery and Function: Insights from Models of Local Unfolding.Journal of molecular biology · 2025Review
- Prediction of enzyme function using an interpretable optimized ensemble learning framework.Chemical science · 2025Article
- Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins.G3 (Bethesda, Md.) · 2025Article
- C11orf54 catalyzes L-xylulose formation in human metabolism.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Measuring catalytic mechanism similarity - a new approach to study enzyme function and evolution.The FEBS journal · 2025Article
- Article
- The Pseudomonas aeruginosa Type VI secretion system toxin Tse8 evolved from a novel N-carbamoylputrescine amidohydrolase.The Biochemical journal · 2025Article
- Phylogenetic history and temperature adaptation contribute to structural and functional stability of proteins in marine mollusks.Communications biology · 2025Article
- Properties of "Stable" Mosquito Cytochrome P450 Enzymes.Insects · 2025Article
- Antibacterial carbon dots.Materials today. Bio · 2025Review
- Paradigms of convergent evolution in enzymes.The FEBS journal · 2025Article
- Artificial Intelligence Methods and Models for Retro-Biosynthesis: A Scoping Review.ACS synthetic biology · 2024Article
- Can genomic signatures guide the selection of host-specific agents for weed biological control?Evolutionary applications · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Enzymes have been shaped by evolution over billions of years to catalyse the chemical reactions that support life on earth. Dispersed in the literature, or organised in online databases, knowledge about enzymes can be structured in distinct dimensions, either related to their quality as biological macromolecules, such as their sequence and structure, or related to their chemical functions, such as the catalytic site, kinetics, mechanism, and overall reaction. The evolution of enzymes can only be understood when each of these dimensions is considered. In addition, many of the properties of enzymes only make sense in the light of evolution. We start this review by outlining the main paradigms of enzyme evolution, including gene duplication and divergence, convergent evolution, and evolution by recombination of domains. In the second part, we overview the current collective knowledge about enzymes, as organised by different types of data and collected in several databases. We also highlight some increasingly powerful computational tools that can be used to close gaps in understanding, in particular for types of data that require laborious experimental protocols. We believe that recent advances in protein structure prediction will be a powerful catalyst for the prediction of binding, mechanism, and ultimately, chemical reactions. A comprehensive mapping of enzyme function and evolution may be attainable in the near future.
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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.