ArticlePloS one2012
Assignment of EC numbers to enzymatic reactions with reaction difference fingerprints.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
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- CLAIRE: a contrastive learning-based predictor for EC number of chemical reactions.Journal of cheminformatics · 2025Article
- Artificial Intelligence Methods and Models for Retro-Biosynthesis: A Scoping Review.ACS synthetic biology · 2024Article
- An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification.Journal of cheminformatics · 2023Article
- Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning.Nature communications · 2023Article
- Complex organic matter degradation by secondary consumers in chemolithoautotrophy-based subsurface geothermal ecosystems.PloS one · 2023Article
- EnzyMine: a comprehensive database for enzyme function annotation with enzymatic reaction chemical feature.Database : the journal of biological databases and curation · 2020Article
- Alignment-Free Method to Predict Enzyme Classes and Subclasses.International journal of molecular sciences · 2019Article
- Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature.BMC bioinformatics · 2018Article
- SimCAL: a flexible tool to compute biochemical reaction similarity.BMC bioinformatics · 2018Article
- Methylglucosylation of aromatic amino and phenolic moieties of drug-like biosynthons by combinatorial biosynthesis.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2018Article
- Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis.Biophysics and physicobiology · 2016Review
- A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks.PLoS computational biology · 2014Article
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Authors and funding
7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The EC numbers represent enzymes and enzyme genes (genomic information), but they are also utilized as identifiers of enzymatic reactions (chemical information). In the present work (ECAssigner), our newly proposed reaction difference fingerprints (RDF) are applied to assign EC numbers to enzymatic reactions. The fingerprints of reactant molecules minus the fingerprints of product molecules will generate reaction difference fingerprints, which are then used to calculate reaction Euclidean distance, a reaction similarity measurement, of two reactions. The EC number of the most similar training reaction will be assigned to an input reaction. For 5120 balanced enzymatic reactions, the RDF with a fingerprint length at 3 obtained at the sub-subclass, subclass, and main class level with cross-validation accuracies of 83.1%, 86.7%, and 92.6% respectively. Compared with three published methods, ECAssigner is the first fully automatic server for EC number assignment. The EC assignment system (ECAssigner) is freely available via: http://cadd.whu.edu.cn/ecassigner/.
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