The web interface, the back-end and the database are deployed as Docker containers, making it easily portable for hosting other sets of NPs and to be deployed on local installations.įull size table Data provenance, model and contentĬOCONUT data has been extracted from 53 various data sources and several manually collected from literature sets, as shown in Table 1. The database can be queried programmatically via a REST API, which facilitates COCONUT integration in workflows. Users can also download the whole dataset or search results in different formats. by molecule name, InChI, InChI key, SMILES, drawn structure, molecular formula), advanced search by molecular features, together with substructure and similarity searches. Its web interface allows diverse simple searches (e.g. The COCONUT database is free and open to all users and there is no login required to access it. Our next step was to make this data available to the scientific community as a full-fledged online natural products database, maintained at. Studies showed that fragments from NPs present in COCONUT have high diversity and structural complexity, which makes it, among other possible applications, a suitable source for drug discovery and can be included in drug design pipelines. ![]() With this ultimate goal in mind, we first assembled the most complete up-to-date COlleCtion of Open Natural ProdUcTs (COCONUT) that we have been continuously curating and annotating. There is, therefore, a need for a generalistic NPs database, that will efficiently aggregate NPs information from various sources, improve its annotation and offer a pleasant user experience. In addition to these relatively big databases, there is a plethora of smaller, more specialized NPs collections, such as FooDB, a user-friendly database hosting a relatively large number of NPs that are found in food. Another major NPs category, plant-produced compounds, also called phytochemicals, is available in several popular and well maintained databases, such as NuBBEDB, KnapSack, CMAUP. Another recent database, NPAtlas, is constantly growing and extremely well annotated, but it is focusing on microbial NPs only. Super Natural II is considered as the largest among all the NP databases, is accessible online in 2020, but it seems not to be maintained anymore and is mainly composed of compounds that can be purchased. For instance, the catalog of NPs from the ZINC database is composed of over 80,000 entries, some of which can be purchased, but apart from their structure and that they are from natural origin, no additional information is provided. The open resources are generally either specialized on a particular type of NPs, either lack annotations. ![]() However, 16% of these are not available online anymore, 40% are commercial and their content cannot be easily accessed. In a recently published review on NPs databases we inventoried over 120 natural products databases that have been published and used in the last 20 years. Natural products (NPs) have received constant attention from the scientific community due to their relevance in drug discovery, chemical ecology and molecular biology in general.
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