ArticleJournal of cheminformatics2021
Classifying natural products from plants, fungi or bacteria using the COCONUT database and machine learning.
Article in Journal of cheminformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 35 citations in OpenAlex.
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- Assigning the stereochemistry of natural products by machine learning.Journal of cheminformatics · 2026Article
- A Structure-Based Deep Learning Framework for Correcting Marine Natural Products' Misannotations Attributed to Host-Microbe Symbiosis.Marine drugs · 2026Article
- An Assessment of Chemical Diversity in Microbial Natural Products.ACS central science · 2025Review
- Biosynfoni: a biosynthesis-informed and interpretable lightweight molecular fingerprint.Journal of cheminformatics · 2025Article
- A Direct Relationship Between 'Blood Stasis' and Fibrinaloid Microclots in Chronic, Inflammatory, and Vascular Diseases, and Some Traditional Natural Products Approaches to Treatment.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Assessing the Inhibitory Potential of Natural Compounds for Targeting the CrtM Proteins in Methicillin-ResistantCurrent medicinal chemistry · 2025Article
- Can large language models predict antimicrobial peptide activity and toxicity?RSC medicinal chemistry · 2024Article
- Effectiveness of molecular fingerprints for exploring the chemical space of natural products.Journal of cheminformatics · 2024Article
- SolPredictor: Predicting Solubility with Residual Gated Graph Neural Network.International journal of molecular sciences · 2024Article
- Machine learning and molecular dynamics simulations predict potential TGR5 agonists for type 2 diabetes treatment.Frontiers in chemistry · 2024Article
- EMNPD: a comprehensive endophytic microorganism natural products database for prompt the discovery of new bioactive substances.Journal of cheminformatics · 2023Article
- Alchemical analysis of FDA approved drugs.Digital discovery · 2023Article
- Structure Elucidation and Biosynthesis of Nannosterols A and B, Myxobacterial Sterols fromJournal of natural products · 2023Article
- Chemoinformatics-driven classification of Angiosperms using sulfur-containing compounds and machine learning algorithm.Plant methods · 2022Article
- Fungal secondary metabolites in food and pharmaceuticals in the era of multi-omics.Applied microbiology and biotechnology · 2022Review
- Transcriptomic and Drug Discovery Analyses Reveal Natural Compounds Targeting the KDM4 Subfamily as Promising Adjuvant Treatments in Cancer.Frontiers in genetics · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Natural products (NPs) represent one of the most important resources for discovering new drugs. Here we asked whether NP origin can be assigned from their molecular structure in a subset of 60,171 NPs in the recently reported Collection of Open Natural Products (COCONUT) database assigned to plants, fungi, or bacteria. Visualizing this subset in an interactive tree-map (TMAP) calculated using MAP4 (MinHashed atom pair fingerprint) clustered NPs according to their assigned origin ( https://tm.gdb.tools/map4/coconut_tmap/ ), and a support vector machine (SVM) trained with MAP4 correctly assigned the origin for 94% of plant, 89% of fungal, and 89% of bacterial NPs in this subset. An online tool based on an SVM trained with the entire subset correctly assigned the origin of further NPs with similar performance ( https://np-svm-map4.gdb.tools/ ). Origin information might be useful when searching for biosynthetic genes of NPs isolated from plants but produced by endophytic microorganisms.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.