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. 2025 Jan 6;53(D1):D634-D643.
doi: 10.1093/nar/gkae1063.

COCONUT 2.0: a comprehensive overhaul and curation of the collection of open natural products database

Venkata Chandrasekhar  1 , Kohulan Rajan  1 , Sri Ram Sagar Kanakam  1 , Nisha Sharma  1 , Viktor Weißenborn  1 , Jonas Schaub  1 , Christoph Steinbeck  1
Affiliations

COCONUT 2.0: a comprehensive overhaul and curation of the collection of open natural products database

Venkata Chandrasekhar et al. Nucleic Acids Res. .

Abstract

The COCONUT (COlleCtion of Open Natural prodUcTs) database was launched in 2021 as an aggregation of openly available natural product datasets and has been one of the biggest open natural product databases since. Apart from the chemical structures of natural products, COCONUT contains information about names and synonyms, species and organism parts in which the natural product has been found, geographic information about where the respective sample has been collected and literature references, where available. COCONUT is openly accessible at https://coconut.naturalproducts.net. Users can search textual information and perform structure, substructure, and similarity searches. The data in COCONUT are available for bulk download as SDF, CSV and a database dump. The web application for accessing the data is open-source. Here, we describe COCONUT 2.0, for which the web application has been completely rewritten, and the data have been newly assembled and extensively curated. New features include data submissions by users and community curation facilitated in various ways.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
Components of an exemplary database record in COCONUT 2.0, which includes its source organism, organism part, chemical structure, geographic information, associated literature, data source collections and further metadata.
Figure 2.
Figure 2.
A compound card entry for caffeine as presented in COCONUT 2.0, showcasing its layout. The compound view includes the NPLikeness score, annotation level, molecular properties, 2D structure and an interactive 3D molecular viewer. Additional details highlight species associations, geolocations and literature references. Furthermore, the card provides links to collections that trace back to the original source datasets, ensuring data provenance, along with an audit trail documenting the entry’s history.
Figure 3.
Figure 3.
NPLikeness score distribution in COCONUT 2.0 (September 2024).
See this image and copyright information in PMC

References

    1. Newman D.J., Cragg G.M.. Natural products as sources of new drugs over the nearly four decades from 01/1981 to 09/2019. J. Nat. Prod. 2020; 83:770–803. - PubMed
    1. Sorokina M., Steinbeck C.. Review on natural products databases: where to find data in 2020. J. Cheminform. 2020; 12:20. - PMC - PubMed
    1. Sorokina M., Merseburger P., Rajan K., Yirik M.A., Steinbeck C.. COCONUT online: COlleCtion of Open Natural prodUcTs database. J. Cheminform. 2021; 13:2. - PMC - PubMed
    1. Wilkinson M.D., Dumontier M., Aalbersberg I. J.J., Appleton G., Axton M., Baak A., Blomberg N., Boiten J.-W., da Silva Santos L.B., Bourne P.E.et al. .. The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data. 2016; 3:160018. - PMC - PubMed
    1. Ertl P., Roggo S., Schuffenhauer A.. Natural product-likeness score and its application for prioritization of compound libraries. J. Chem. Inf. Model. 2008; 48:68–74. - PubMed

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