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XMetDB: an open access database for xenobiotic metabolism
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0002-8083-2864
Department of Drug Design and Pharmacology, University of Copenhagen.
Department of Bioinformatics - BiGCaT, Maastricht University.
Department of Bioinformatics - BiGCaT, Maastricht University.
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2016 (English)In: Journal of Cheminformatics, ISSN 1758-2946, E-ISSN 1758-2946, Vol. 8, 47Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2016. Vol. 8, 47
Keyword [en]
Xenobiotic; Metabolism; Database; Cytochrome; P450
National Category
Bioinformatics (Computational Biology)
Research subject
Bioinformatics
Identifiers
URN: urn:nbn:se:uu:diva-303684DOI: 10.1186/s13321-016-0161-3ISI: 000383831000001PubMedID: 27651835OAI: oai:DiVA.org:uu-303684DiVA: diva2:972671
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceStiftelsen Olle Engkvist ByggmästareeSSENCE - An eScience Collaboration
Available from: 2016-09-22 Created: 2016-09-22 Last updated: 2016-10-19Bibliographically approved

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Spjuth, Ola
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