ArticleBioinformatics (Oxford, England)2023
TopEnzyme: a framework and database for structural coverage of the functional enzyme space.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Sustainable production of glutaric acid in microbial cell factories: Current advances and future prospects.Synthetic and systems biotechnology · 2026Review
- OneProt: Towards multi-modal protein foundation models via latent space alignment of sequence, structure, binding sites and text encoders.PLoS computational biology · 2025Article
- TopEC: prediction of Enzyme Commission classes by 3D graph neural networks and localized 3D protein descriptor.Nature communications · 2025Article
- Enzyme Databases in the Era of Omics and Artificial Intelligence.International journal of molecular sciences · 2023Review
- Expression of Phospholipase D Family Member 6 in Bovine Testes and Its Molecular Characteristics.International journal of molecular sciences · 2023Article
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2 authors.
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Abstract
motivationTopEnzyme is a database of structural enzyme models created with TopModel and is linked to the SWISS-MODEL repository and AlphaFold Protein Structure Database to provide an overview of structural coverage of the functional enzyme space for over 200 000 enzyme models. It allows the user to quickly obtain representative structural models for 60% of all known enzyme functions.
resultsWe assessed the models with TopScore and contributed 9039 good-quality and 1297 high-quality structures. Furthermore, we compared these models to AlphaFold2 models with TopScore and found that the TopScore differs only by 0.04 on average in favor of AlphaFold2. We tested TopModel and AlphaFold2 for targets not seen in the respective training databases and found that both methods create qualitatively similar structures. When no experimental structures are available, this database will facilitate quick access to structural models across the currently most extensive structural coverage of the functional enzyme space within Swiss-Prot. AVAILABILITY AND IMPLEMENTATION: We provide a full web interface to the database at https://cpclab.uni-duesseldorf.de/topenzyme/.
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