Cheminformatics Microservice: unifying access to open cheminformatics toolkits

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 compa...

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Vydáno v:Journal of cheminformatics Ročník 15; číslo 1; s. 98 - 11
Hlavní autoři: Chandrasekhar, Venkata, Sharma, Nisha, Schaub, Jonas, Steinbeck, Christoph, Rajan, Kohulan
Médium: Journal Article
Jazyk:angličtina
Vydáno: Cham Springer International Publishing 16.10.2023
Springer Nature B.V
BMC
Témata:
CDK
Cheminformatics
Chemistry
Chemistry and Materials Science
Computational Biology/Bioinformatics
Computer Applications in Chemistry
Documentation and Information in Chemistry
Improving Reproducibility and Reusability in the Journal of Cheminformatics
Informatics
Microservice
Open Babel
Open source software
RDKit
Software
Source code
Theoretical and Computational Chemistry
Toolkits
Version control
Toolkits
Cheminformatics
Microservice
CDK
Open Babel
RDKit
ISSN:1758-2946, 1758-2946
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Popis
Shrnutí: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
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ISSN:1758-2946
1758-2946
DOI:10.1186/s13321-023-00762-4