ReviewTrends in biochemical sciences2014
Leveraging structure for enzyme function prediction: methods, opportunities, and challenges.
Review in Trends in biochemical sciences, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- EnzymeHunter: Achieving fine-grained enzyme function prediction with a hierarchically aware contrastive learning framework.Patterns (New York, N.Y.) · 2026Article
- Constructing gene co-functional and co-regulatory networks from public transcriptomes using condition-specific ensemble co-expression.Nature communications · 2026Article
- Special Issue "Mechanism of Enzyme Catalysis: When Structure Meets Function".International journal of molecular sciences · 2026Article
- Leucine Aminopeptidase fromBiomolecules · 2026Article
- Discovery of a non-canonical prototype long-chain monoacylglycerol lipase through a structure-based endogenous reaction intermediate complex.Nature communications · 2023Article
- PCPD: Plant cytochrome P450 database and web-based tools for structural construction and ligand docking.Synthetic and systems biotechnology · 2021Article
- Chemometric Models of Differential Amino Acids at the NaMolecules (Basel, Switzerland) · 2020Article
- Article
- Article
- Confronting the catalytic dark matter encoded by sequenced genomes.Nucleic acids research · 2017Article
- Molecular characterization of two Rhesus glycoproteins from the euryhaline freshwater white-rimmed stingray, Himantura signifer, and changes in their transcript levels and protein abundance in the gills, kidney, and liver during brackish water acclimation.Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology · 2017Article
- Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin.Biochemistry · 2017Article
- Article
- Perspective: Quantum mechanical methods in biochemistry and biophysics.The Journal of chemical physics · 2016Article
- Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027.The Journal of antibiotics · 2016Article
- Defining the Product Chemical Space of Monoterpenoid Synthases.PLoS computational biology · 2016Article
- The enzymatic nature of an anonymous protein sequence cannot reliably be inferred from superfamily level structural information alone.Protein science : a publication of the Protein Society · 2015Article
- Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach.PLoS computational biology · 2014Article
- QM/MM free energy simulations: recent progress and challenges.Molecular simulationArticle
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The rapid growth of the number of protein sequences that can be inferred from sequenced genomes presents challenges for function assignment, because only a small fraction (currently <1%) has been experimentally characterized. Bioinformatics tools are commonly used to predict functions of uncharacterized proteins. Recently, there has been significant progress in using protein structures as an additional source of information to infer aspects of enzyme function, which is the focus of this review. Successful application of these approaches has led to the identification of novel metabolites, enzyme activities, and biochemical pathways. We discuss opportunities to elucidate systematically protein domains of unknown function, orphan enzyme activities, dead-end metabolites, and pathways in secondary metabolism.
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Registered trials
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