Abstract:Sesquiterpenoids with a cage-like multiring frame are rarely found in nature. Mining of the isopod-derived fungus Aspergillus parasiticus SDU001 by the one strain−many compounds (OSMAC) strategy unexpectedly led to the discovery of fungal drimane-type sesquiterpenoids astellolide R (1), featuring an unusual cage-like 6/6/5/6/5 pentacyclic ring system, astellolide S (2), possessing a rare nicotinic acid building block, and astellolides T−W (3−6). Their structures were comprehensively assigned by spectroscopic d… Show more
“… Fig. 3 The molecule Astellolide W [ 60 ] was extracted from the referenced article using DECIMER. The structure is depicted using ChemDraw ( A ) and CDK ( B ) for 2D representations, while the 3D depiction ( C ) was created using the presented microservice …”
In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various cheminformatics programming toolkits. However, adopting these toolkits presents challenges, including proper installation, setup, deployment, and compatibility management. In this work, we present the Cheminformatics Microservice. This open-source solution provides a unified interface for accessing commonly used functionalities of multiple cheminformatics toolkits, namely RDKit, Chemistry Development Kit (CDK), and Open Babel. In addition, more advanced functionalities like structure generation and Optical Chemical Structure Recognition (OCSR) are made available through the Cheminformatics Microservice based on pre-existing tools. The software service also enables developers to extend the functionalities easily and to seamlessly integrate them with existing workflows and applications. It is built on FastAPI and containerized using Docker, making it highly scalable. An instance of the microservice is publicly available at https://api.naturalproducts.net. The source code is publicly accessible on GitHub, accompanied by comprehensive documentation, version control, and continuous integration and deployment workflows. All resources can be found at the following link: https://github.com/Steinbeck-Lab/cheminformatics-microservice.
Graphical Abstract
“… Fig. 3 The molecule Astellolide W [ 60 ] was extracted from the referenced article using DECIMER. The structure is depicted using ChemDraw ( A ) and CDK ( B ) for 2D representations, while the 3D depiction ( C ) was created using the presented microservice …”
In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various cheminformatics programming toolkits. However, adopting these toolkits presents challenges, including proper installation, setup, deployment, and compatibility management. In this work, we present the Cheminformatics Microservice. This open-source solution provides a unified interface for accessing commonly used functionalities of multiple cheminformatics toolkits, namely RDKit, Chemistry Development Kit (CDK), and Open Babel. In addition, more advanced functionalities like structure generation and Optical Chemical Structure Recognition (OCSR) are made available through the Cheminformatics Microservice based on pre-existing tools. The software service also enables developers to extend the functionalities easily and to seamlessly integrate them with existing workflows and applications. It is built on FastAPI and containerized using Docker, making it highly scalable. An instance of the microservice is publicly available at https://api.naturalproducts.net. The source code is publicly accessible on GitHub, accompanied by comprehensive documentation, version control, and continuous integration and deployment workflows. All resources can be found at the following link: https://github.com/Steinbeck-Lab/cheminformatics-microservice.
Graphical Abstract
“…Drimane-type sesquiterpenes are a class of natural products with a bicyclic skeleton, which are widely distributed in eukaryotes and have diverse biological activities, such as anti-inflammatory, antibacterial, and cytotoxic activities. 27,153–157 At present, drimane-type sesquiterpenes from fungi mainly include two types, one is characterized by a C8–C9 double bond, and the other is characterized by a C7–C8 double bond. In 2016, the gene cluster responsible for the biosynthesis of astellolides featuring a C8–C9 double bond was first identified in A. oryzae RIB40.…”
Section: Tailoring Enzymes In Fungal Terpenoid Biosynthesismentioning
confidence: 99%
“…1). 24–27 The development of high-throughput sequencing technology has facilitated the use of genome mining as an effective strategy for discovering novel terpenoids through the heterologous expression of terpenoid cyclases and related tailoring enzymes in Escherichia coli , Saccharomyces cerevisiae , and filamentous fungi such as Aspergillus oryzae and A . nidulans .…”
This review covers all fungal terpenoid cyclases (TCs), including class I and II TCs as well as emerging UbiA-type TCs, together with their tailoring enzymes, focusing on newly identified TCs and tailoring enzymes from 2015 to August 2023.
“…Helm Chart or the Docker Compose file provided in the codebase enable scaling Fig. 3 The molecule Astellolide W [60] was extracted from the referenced article using DECIMER. The structure is depicted using ChemDraw (A) and CDK (B) for 2D representations, while the 3D depiction (C) was created using the presented microservice without any additional setup.…”
In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various cheminformatics programming toolkits. However, adopting these toolkits presents challenges, including proper installation, setup, deployment, and compatibility management. In this work, we present the Cheminformatics Microservice. This open-source solution provides a unified interface for accessing commonly used functionalities of multiple cheminformatics toolkits, namely RDKit, Chemistry Development Kit (CDK), and Open Babel. In addition, more advanced functionalities like structure generation and Optical Chemical Structure Recognition (OCSR) are made available through the Cheminformatics Microservice based on pre-existing tools. The software service also enables developers to extend the functionalities easily and to seamlessly integrate them with existing workflows and applications. It is built on FastAPI and containerized using Docker, making it highly scalable. An instance of the microservice is publicly available at https://api.naturalproducts.net. The source code is publicly accessible on GitHub, accompanied by comprehensive documentation, version control, and continuous integration and deployment workflows. All resources can be found at the following link: https://github.com/Steinbeck-Lab/cheminformatics-microservice.
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