Please use this identifier to cite or link to this item:
doi:10.22028/D291-41223
Title: | HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search |
Author(s): | Lee, Yi-Yuan Guler, Mustafa Chigumba, Desnor N. Wang, Shen Mittal, Neel Miller, Cameron Krummenacher, Benjamin Liu, Haodong Cao, Liu Kannan, Aditya Narayan, Keshav Slocum, Samuel T. Roth, Bryan L. Gurevich, Alexey Behsaz, Bahar Kersten, Roland D. Mohimani, Hosein |
Language: | English |
Title: | Nature Communications |
Volume: | 14 |
Issue: | 1 |
Publisher/Platform: | Springer Nature |
Year of Publication: | 2023 |
Free key words: | Computational platforms and environments Drug discovery and development Natural products Peptides |
DDC notations: | 004 Computer science, internet |
Publikation type: | Journal Article |
Abstract: | Recent analyses of public microbial genomes have found over a million biosynthetic gene clusters, the natural products of the majority of which remain unknown. Additionally, GNPS harbors billions of mass spectra of natural products without known structures and biosynthetic genes. We bridge the gap between large-scale genome mining and mass spectral datasets for natural product discovery by developing HypoRiPPAtlas, an Atlas of hypothetical natural product structures, which is ready-to-use for in silico database search of tandem mass spectra. HypoRiPPAtlas is constructed by mining genomes using seq2ripp, a machine-learning tool for the prediction of ribosomally synthesized and post-translationally modified peptides (RiPPs). In HypoRiPPAtlas, we identify RiPPs in microbes and plants. HypoRiPPAtlas could be extended to other natural product classes in the future by implementing corresponding biosynthetic logic. This study paves the way for large-scale explorations of biosynthetic pathways and chemical structures of microbial and plant RiPP classes. |
DOI of the first publication: | 10.1038/s41467-023-39905-4 |
URL of the first publication: | https://doi.org/10.1038/s41467-023-39905-4 |
Link to this record: | urn:nbn:de:bsz:291--ds-412231 hdl:20.500.11880/36974 http://dx.doi.org/10.22028/D291-41223 |
ISSN: | 2041-1723 |
Date of registration: | 27-Nov-2023 |
Description of the related object: | Supplementary information |
Related object: | https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-023-39905-4/MediaObjects/41467_2023_39905_MOESM1_ESM.pdf https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-023-39905-4/MediaObjects/41467_2023_39905_MOESM2_ESM.pdf |
Faculty: | MI - Fakultät für Mathematik und Informatik |
Department: | MI - Informatik |
Professorship: | MI - Jun.-Prof. Alexey Gurevich |
Collections: | SciDok - Der Wissenschaftsserver der Universität des Saarlandes |
Files for this record:
File | Description | Size | Format | |
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s41467-023-39905-4.pdf | 1,82 MB | Adobe PDF | View/Open |
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