ReviewProtein science : a publication of the Protein Society2022
Capturing the geometry, function, and evolution of enzymes with 3D templates.
Review in Protein science : a publication of the Protein Society, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Investigating enzyme function by geometric matching of catalytic motifs.Protein science : a publication of the Protein Society · 2026Article
- Measuring catalytic mechanism similarity - a new approach to study enzyme function and evolution.The FEBS journal · 2025Article
- Paradigms of convergent evolution in enzymes.The FEBS journal · 2025Article
- Heavy Metal Contamination: Sources, Health Impacts, and Sustainable Mitigation Strategies with Insights from Nigerian Case Studies.F1000Research · 2025Review
- Back in time to the Gly-rich prototype of the phosphate binding elementary function.Current research in structural biology · 2024Review
- ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration.Bioinformatics advances · 2024Article
- Enzyme function and evolution through the lens of bioinformatics.The Biochemical journal · 2023Review
- Current successes and remaining challenges in protein function prediction.Frontiers in bioinformatics · 2023Article
- Capturing the geometry, function, and evolution of enzymes with 3D templates.Protein science : a publication of the Protein Society · 2022Review
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Authors and funding
2 authors.
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Abstract
Structural templates are 3D signatures representing protein functional sites, such as ligand binding cavities, metal coordination motifs, or catalytic sites. Here we explore methods to generate template libraries and algorithms to query structures for conserved 3D motifs. Applications of templates are discussed, as well as some exemplar cases for examining evolutionary links in enzymes. We also introduce the concept of using more than one template per structure to represent flexible sites, as an approach to better understand catalysis through snapshots captured in enzyme structures. Functional annotation from structure is an important topic that has recently resurfaced due to the new more accurate methods of protein structure prediction. Therefore, we anticipate that template-based functional site detection will be a powerful tool in the task of characterizing a vast number of new protein models.
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