mlsanityData to 7 Oct 2026

ReactZyme: A Benchmark for Enzyme-Reaction Prediction

arXiv 2408.13659 ↗First posted 24 Aug 2024cs.LG cs.AI cs.CEcited by 13

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Abstract (arXiv)

Enzymes, with their specific catalyzed reactions, are necessary for all aspects of life, enabling diverse biological processes and adaptations. Predicting enzyme functions is essential for understanding biological pathways, guiding drug development, enhancing bioproduct yields, and facilitating evolutionary studies. Addressing the inherent complexities, we introduce a new approach to annotating enzymes based on their catalyzed reactions. This method provides detailed insights into specific reactions and is adaptable to newly discovered reactions, diverging from traditional classifications by protein family or expert-derived reaction classes. We employ machine learning algorithms to analyze enzyme reaction datasets, delivering a much more refined view on the functionality of enzymes. Our evaluation leverages the largest enzyme-reaction dataset to date, derived from the SwissProt and Rhea databases with entries up to January 8, 2024. We frame the enzyme-reaction prediction as a retrieval problem, aiming to rank enzymes by their catalytic ability for specific reactions. With our model, we can recruit proteins for novel reactions and predict reactions in novel proteins, facilitating enzyme discovery and function annotation (https://github.com/WillHua127/ReactZyme).

Key facts. Cited by 13 papers in the map (data through 7 Oct 2026). Builds on 23 of its 83 references that are in the map. First posted on arXiv 24 Aug 2024.

Builds on

23 of 83 references.

References · 23

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11 more
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Cited by year (2026 to 7 Oct)

Citing papers per year: 2024: 3; 2025: 7; 2026: 3.

13 papers.

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  1. 2025Computational Protein Science in the Era of Large Language Models (LLMs)cited by 6
  2. 2024EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamicscited by 5
  3. 2024Revealing the Pitfalls and Re-Evaluating the Advancement of Heterophilic Graph Learningcited by 3
  4. 2024Reaction-conditioned De Novo Enzyme Design with GENzymecited by 3
  5. 2025UniZyme: A Unified Protein Cleavage Site Predictor Enhanced with Enzyme Active-Site Knowledgecited by 3
  6. 2025Advances in Protein Representation Learning: Methods, Applications, and Future Directionscited by 3
  7. 2025EnzyControl: Adding Functional and Substrate-Specific Control for Enzyme Backbone Generationcited by 1
  8. 2026Improving Enzyme Prediction with Chemical Reaction Equations by Hypergraph-Enhanced Knowledge Graph Embeddingscited by 1
  9. 2025AlphaFold Database Debiasing for Robust Inverse Foldingcited by 0
  10. 2025Exploring Heterophily in Graph-level Taskscited by 0
  11. 2025Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrievalcited by 0
  12. 2026TIGER: Text-Informed Generalized Enzyme-Reaction Retrievalcited by 0
1 more
  1. 2026Retrieval-Augmented Multimodal Learning for Enzyme-Substrate Interaction Prediction Under Low-Homology Shiftcited by 0