ReviewCurrent opinion in chemical biology2011
Toward mechanistic classification of enzyme functions.
Review in Current opinion in chemical biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Profiling tear film enzymes reveals major metabolic pathways involved in the homeostasis of the ocular surface.Scientific reports · 2023Article
- Learning graph representations of biochemical networks and its application to enzymatic link prediction.Bioinformatics (Oxford, England) · 2021Article
- A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function.Database : the journal of biological databases and curation · 2020Article
- Effusion: prediction of protein function from sequence similarity networks.Bioinformatics (Oxford, England) · 2019Article
- SimCAL: a flexible tool to compute biochemical reaction similarity.BMC bioinformatics · 2018Article
- A global view of structure-function relationships in the tautomerase superfamily.The Journal of biological chemistry · 2018Article
- Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- AGeNNT: annotation of enzyme families by means of refined neighborhood networks.BMC bioinformatics · 2017Article
- An assessment of catalytic residue 3D ensembles for the prediction of enzyme function.BMC bioinformatics · 2015Article
- Application of a hierarchical enzyme classification method reveals the role of gut microbiome in human metabolism.BMC genomics · 2015Article
- Nonenzymatic Reactions above Phospholipid Surfaces of Biological Membranes: Reactivity of Phospholipids and Their Oxidation Derivatives.Oxidative medicine and cellular longevity · 2015Review
- New insights about enzyme evolution from large scale studies of sequence and structure relationships.The Journal of biological chemistry · 2014Review
- The evolution of enzyme function in the isomerases.Current opinion in structural biology · 2014Review
- The natural history of biocatalytic mechanisms.PLoS computational biology · 2014Article
- Enzyme recruitment and its role in metabolic expansion.Biochemistry · 2014Review
- Div-BLAST: diversification of sequence search results.PloS one · 2014Article
- The Structure-Function Linkage Database.Nucleic acids research · 2014Article
- High-throughput functional screening of steroid substrates with wild-type and chimeric P450 enzymes.BioMed research international · 2014Article
- Article
- Is EC class predictable from reaction mechanism?BMC bioinformatics · 2012Article
Corrections and comments
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2 authors.
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Abstract
Classification of enzyme function should be quantitative, computationally accessible, and informed by sequences and structures to enable use of genomic information for functional inference and other applications. Large-scale studies have established that divergently evolved enzymes share conserved elements of structure and common mechanistic steps and that convergently evolved enzymes often converge to similar mechanisms too, suggesting that reaction mechanisms could be used to develop finer-grained functional descriptions than provided by the Enzyme Commission (EC) system currently in use. Here we describe how evolution informs these structure-function mappings and review the databases that store mechanisms of enzyme reactions along with recent developments to measure ligand and mechanistic similarities. Together, these provide a foundation for new classifications of enzyme function.
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