ArticleJournal of cheminformatics2016
XMetDB: an open access database for xenobiotic metabolism.
Article in Journal of cheminformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Artificial intelligence and computational methods in human metabolism research: A comprehensive survey.Journal of pharmaceutical analysis · 2025Review
- MetSim: Integrated Programmatic Access and Pathway Management for Xenobiotic Metabolism Simulators.Chemical research in toxicology · 2024Article
- Comparison and summary of in silico prediction tools for CYP450-mediated drug metabolism.Drug discovery today · 2023Review
- Identifying xenobiotic metabolites withFrontiers in toxicology · 2023Article
- Uncovering PFAS and Other Xenobiotics in the Dark Metabolome Using Ion Mobility Spectrometry, Mass Defect Analysis, and Machine Learning.Environmental science & technology · 2022Article
- Metabolomic Approaches to Study Chemical Exposure-Related Metabolism Alterations in Mammalian Cell Cultures.International journal of molecular sciences · 2020Review
- BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification.Journal of cheminformatics · 2019Article
- Review
Corrections and comments
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Authors and funding
5 authors.
Funding
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Abstract
Xenobiotic metabolism is an active research topic but the limited amount of openly available high-quality biotransformation data constrains predictive modeling. Current database often default to commonly available information: which enzyme metabolizes a compound, but neither experimental conditions nor the atoms that undergo metabolization are captured. We present XMetDB, an open access database for drugs and other xenobiotics and their respective metabolites. The database contains chemical structures of xenobiotic biotransformations with substrate atoms annotated as reaction centra, the resulting product formed, and the catalyzing enzyme, type of experiment, and literature references. Associated with the database is a web interface for the submission and retrieval of experimental metabolite data for drugs and other xenobiotics in various formats, and a web API for programmatic access is also available. The database is open for data deposition, and a curation scheme is in place for quality control. An extensive guide on how to enter experimental data into is available from the XMetDB wiki. XMetDB formalizes how biotransformation data should be reported, and the openly available systematically labeled data is a big step forward towards better models for predictive metabolism.
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Registered trials
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