NP-MRD: the Natural Products Magnetic Resonance Database

Abstract

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.

CFM-ID 4.0 – a web server for accurate MS-based metabolite identification

“…In particular, a number of improvements were made including: modernizing the web server's appearance, simplifying the workflow, providing a more comprehensive and easier-to-understand Help section, and most importantly, offering a better interactive display of the MS/MS spectra. More specifically, we redesigned CFM-ID 4.0’s Home Page , so that it now shares the same layout and styling with our other popular databases and web servers such as HMDB 5.0 ( 6 ) and NP-MRD ( 39 ). This re-worked home page is more self-explanatory and straightforward than the previous design.…”

Dereplication of Fungal Metabolites by NMR-Based Compound Networking Using MADByTE

“…The evolution of new, highly accurate computational methods for prediction of NMR spectra , has the potential to eliminate, or at least soften, this barrier. An initiative, termed the natural product magnetic resonance database (NP-MRD, ), aims to provide NMR shift predictions in popular solvents for thousands of natural product compounds using these high-accuracy prediction and spectra simulation utilities . These advancements and community-driven efforts offer an enticing prospect for the expanded use of NMR-based dereplication methods in the coming years.…”

NMR and Metabolomics—A Roadmap for the Future

“…Several substantial NMR databases are now available that allow searching of 1D and 2D NMR data for individual metabolites. These include the Human Metabolome Database (HMDB) [ 127 ], the Madison-Qingdao Metabolomics Consortium Database (MQMCD), the Biological Magnetic Resonance Bank (BMRB) [ 128 , 129 ], and more recently, the Natural Product Magnetic Resonance Database (NP-MRD) [ 130 ]. We encourage all to contribute to these valuable community resources to help expand their utility.…”