NP-MRD: the Natural Products Magnetic Resonance Database.


Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
07 01 2022
Historique:
accepted: 19 10 2021
revised: 15 10 2021
received: 15 08 2021
pubmed: 19 11 2021
medline: 24 2 2022
entrez: 18 11 2021
Statut: ppublish

Résumé

The Natural Products Magnetic Resonance Database (NP-MRD) is a comprehensive, freely available electronic resource for the deposition, distribution, searching and retrieval of nuclear magnetic resonance (NMR) data on natural products, metabolites and other biologically derived chemicals. NMR spectroscopy has long been viewed as the 'gold standard' for the structure determination of novel natural products and novel metabolites. NMR is also widely used in natural product dereplication and the characterization of biofluid mixtures (metabolomics). All of these NMR applications require large collections of high quality, well-annotated, referential NMR spectra of pure compounds. Unfortunately, referential NMR spectral collections for natural products are quite limited. It is because of the critical need for dedicated, open access natural product NMR resources that the NP-MRD was funded by the National Institute of Health (NIH). Since its launch in 2020, the NP-MRD has grown quickly to become the world's largest repository for NMR data on natural products and other biological substances. It currently contains both structural and NMR data for nearly 41,000 natural product compounds from >7400 different living species. All structural, spectroscopic and descriptive data in the NP-MRD is interactively viewable, searchable and fully downloadable in multiple formats. Extensive hyperlinks to other databases of relevance are also provided. The NP-MRD also supports community deposition of NMR assignments and NMR spectra (1D and 2D) of natural products and related meta-data. The deposition system performs extensive data enrichment, automated data format conversion and spectral/assignment evaluation. Details of these database features, how they are implemented and plans for future upgrades are also provided. The NP-MRD is available at https://np-mrd.org.

Identifiants

pubmed: 34791429
pii: 6430498
doi: 10.1093/nar/gkab1052
pmc: PMC8728158
doi:

Substances chimiques

Biological Products 0

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

D665-D677

Subventions

Organisme : NCCIH NIH HHS
ID : U24 AT010811
Pays : United States

Informations de copyright

© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

Références

J Chem Theory Comput. 2021 Feb 9;17(2):826-840
pubmed: 33428408
Nucleic Acids Res. 2012 Jan;40(Database issue):D136-43
pubmed: 22139910
Bioinformatics. 2007 Dec 1;23(23):3256-7
pubmed: 17956876
Phytochemistry. 2004 Oct;65(19):2711-7
pubmed: 15464159
Nat Prod Rep. 2013 Apr;30(4):501-24
pubmed: 23291908
Nucleic Acids Res. 2018 Jan 4;46(D1):D608-D617
pubmed: 29140435
Anal Chem. 2018 Jan 2;90(1):649-656
pubmed: 29035042
Nat Prod Rep. 2019 Jan 1;36(1):35-107
pubmed: 30003207
Magn Reson Chem. 2018 Jun;56(6):520-528
pubmed: 28981966
J Cheminform. 2018 Oct 26;10(1):52
pubmed: 30367288
ACS Cent Sci. 2019 Nov 27;5(11):1824-1833
pubmed: 31807684
Curr Opin Biotechnol. 2014 Feb;25:1-7
pubmed: 24484874
Nucleic Acids Res. 2018 Jan 4;46(D1):D1074-D1082
pubmed: 29126136
J Cheminform. 2020 Apr 3;12(1):20
pubmed: 33431011
Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8
pubmed: 17984079
J Nat Prod. 2020 Mar 27;83(3):770-803
pubmed: 32162523
Chin J Nat Med. 2013 May;11(3):193-8
pubmed: 23725829
Sci Data. 2016 Mar 15;3:160018
pubmed: 26978244
Phytochemistry. 2015 May;113:87-95
pubmed: 25534952
J Cheminform. 2016 Nov 4;8:61
pubmed: 27867422
Plant Cell Physiol. 2012 Feb;53(2):e1
pubmed: 22123792
Magn Reson Chem. 2015 Aug;53(8):582-9
pubmed: 25998807
Fortune. 2015 May 1;171(6):16
pubmed: 26242136
J Magn Reson. 2011 Feb;208(2):179-94
pubmed: 21169043
Anal Chem. 2002 Jan 1;74(1):80-90
pubmed: 11795822
Structure. 2013 Sep 3;21(9):1563-70
pubmed: 24010715
Nucleic Acids Res. 2017 Jan 4;45(D1):D440-D445
pubmed: 27899612

Auteurs

David S Wishart (DS)

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada.
Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada.
Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2H7, Canada.

Zinat Sayeeda (Z)

Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada.

Zachary Budinski (Z)

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

AnChi Guo (A)

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Brian L Lee (BL)

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Mark Berjanskii (M)

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Manoj Rout (M)

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Harrison Peters (H)

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Raynard Dizon (R)

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Robert Mah (R)

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Claudia Torres-Calzada (C)

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Mickel Hiebert-Giesbrecht (M)

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Dorna Varshavi (D)

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Dorsa Varshavi (D)

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Eponine Oler (E)

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Dana Allen (D)

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Xuan Cao (X)

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Vasuk Gautam (V)

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Andrew Maras (A)

Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.

Ella F Poynton (EF)

Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.

Pegah Tavangar (P)

Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.

Vera Yang (V)

Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.

Jeffrey A van Santen (JA)

Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.

Rajarshi Ghosh (R)

Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
MU Metabolomics Center, University of Missouri, Columbia, MO 65211, USA.
Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.

Saurav Sarma (S)

Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
MU Metabolomics Center, University of Missouri, Columbia, MO 65211, USA.
Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.

Eleanor Knutson (E)

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.

Victoria Sullivan (V)

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.

Amy M Jystad (AM)

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.

Ryan Renslow (R)

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.

Lloyd W Sumner (LW)

Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
MU Metabolomics Center, University of Missouri, Columbia, MO 65211, USA.
Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.

Roger G Linington (RG)

Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.

John R Cort (JR)

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.

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Classifications MeSH