The Natural Products Magnetic Resonance Database (NP-MRD) for 2025.

Scott Han, Roger G Linington, Jessica L Bade, Niranjan Govind, Amy M Jystad, Lillian R Stillwell, Hailey A Shreffler, James T Koller, Zachary M Tretter, Benjamin Ledingham, Jonghyeok Kim, Tamara Jordan, Vasuk Gautam, Harrison Peters, Eponine Oler, Brian L Lee, Ella F Poynton, Matthew Pin, Lloyd W Sumner, David S Wishart, Sukanta Saha, John R Cort, An Chi Guo, Tanvir Sajed, Mark Berjanskii, Zinat Sayeeda, Bharat Goel

Journal: Nucleic acids research 2025;53(D1):D700-D708

PMID: 39574402

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Abstract

The Natural Products Magnetic Resonance Database (NP-MRD; https://np-mrd.org) is a comprehensive, freely accessible, web-based resource for the deposition, distribution, extraction, and retrieval of nuclear magnetic resonance (NMR) data on natural products (NPs). The NP-MRD was initially established to support compound de-replication and data dissemination for the NP community. However, that community has now grown to include many users from the metabolomics, microbiomics, foodomics, and nutrition science fields. Indeed, since its launch in 2022, the NP-MRD has expanded enormously in size, scope, and popularity. The current version of NP-MRD now contains nearly 7× more compounds (281 859 versus 40 908) and 7× more NMR spectra (5.5 million versus 817 278) than the first release. More specifically, an additional 4.6 million predicted spectra and another 11 000 spectra simulated from experimental chemical shifts were deposited into the database. Likewise, the number of NMR raw spectral data depositions has grown from 165 spectra per year to >10 000 per year. As a result of this expansion, the number of monthly webpage views has grown from 55 to 20 000 and the number of monthly visitors has increased from 7 to 2500. To address this growth and to better support the expanding needs of its diverse community of users, many additional improvements to the NP-MRD have been made. These include significant enhancements to the data submission process, notable updates to the database's spectral search utilities and useful additions to support better NMR spectral analysis/prediction. Significant efforts have also been undertaken to remediate and update many of NP-MRD's database entries. This manuscript describes these database improvements and expansion efforts, along with how they have been implemented and what future upgrades to the NP-MRD are planned.

Address: 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.; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.; Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.; Department of Biochemistry, Bond Life Sciences Center, and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA.; Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada.; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.; Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.; Chemical and Biological Signatures, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.; Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA.

DOI: 10.1093/nar/gkae1067