ArticleNature communications2023
HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Advances in tools, strategies, and applications of mining of microbial genomes for novel antimicrobials: a comprehensive review.Folia microbiologica · 2026Review
- Advances in Natural Product Extraction: Established and Emerging Technologies.Molecules (Basel, Switzerland) · 2026Review
- Marine natural products.Natural product reports · 2026Review
- MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis.Nucleic acids research · 2026Article
- Emerging strategies to enhance microbial natural product-based drug discovery.Current opinion in biotechnology · 2025Review
- Seq2Saccharide: Discovering Oligosaccharides and Aminoglycosides Natural Products by Integrating Computational Mass Spectrometry and Genome Mining.Journal of the American Chemical Society · 2025Article
- Microbial secondary metabolites: advancements to accelerate discovery towards application.Nature reviews. Microbiology · 2025Review
- Synthetic Biology in Natural Product Biosynthesis.Chemical reviews · 2025Review
- Aromatic side-chain crosslinking in RiPP biosynthesis.Nature chemical biology · 2025Review
- Plant genome mining of burpitides from fused precursor peptides.Methods in enzymology · 2025Article
- Plant peptides - redefining an area of ribosomally synthesized and post-translationally modified peptides.Natural product reports · 2024Review
- Discovering type I cis-AT polyketides through computational mass spectrometry and genome mining with Seq2PKS.Nature communications · 2024Article
- Proteases Involved in Leader Peptide Removal during RiPP Biosynthesis.ACS bio & med chem Au · 2024Review
- Mining raw plant transcriptomic data for new cyclopeptide alkaloids.Beilstein journal of organic chemistry · 2024Article
- HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search.Nature communications · 2023Article
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Authors and funding
17 authors.
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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.
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