Over a decade ago, when installing cheminformatics toolkits like RDKit was not for the faint-hearted, Michał Nowotka from our team created Beaker — a lightweight web service that exposed RDKit functionality via a simple REST API. The goal was simple: make it easy for anyone to perform cheminformatics operations without having to wrestle with complex build chains, platform quirks, or dependency headaches.
For many researchers, Beaker became a convenient gateway into the world of cheminformatics, enabling structure standardisation, property calculation, and more — all without a local installation of RDKit.
Why We’re Shutting It Down
The landscape today is very different from when Beaker was first released. Installing RDKit has become dramatically simpler, thanks to well-maintained conda packages and PyPI distributions, as well as clear documentation across platforms. With these improvements, the original need for Beaker has largely disappeared.
Maintaining Beaker still requires developer time and infrastructure resources — effort we believe is better spent on maintaining and improving other core ChEMBL services and data resources. For this reason, Beaker will be retired on 1 September.
Alternatives
If you still prefer to use RDKit functionality as a web service rather than installing it locally, we recommend exploring the Cheminformatics Microservice developed by Kohulan Rajan at the Steinbeck Lab at Friedrich Schiller University Jena. It offers a similar approach to programmatically accessing cheminformatics features via an API. If you’re interested in the Beaker code itself, it is available here.
Thank You
We’d like to thank all the users who have relied on Beaker over the years, sent feedback, and helped shape its capabilities.
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