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Improvements in SureChEMBL's chemistry search and adoption of RDKit

By Eloy


 

 

Dear SureChEMBL users,

If you frequently rely on our "chemistry search" feature, today brings great news! We’ve recently implemented a major update that makes your search experience faster than ever.


What's New?

Last week, we upgraded our structure search engine by aligning it with the core code base used in ChEMBL. This update allows SureChEMBL to leverage our FPSim2 Python package, returning results in approximately one second. The similarity search relies on 256-bit RDKit-calculated ECFP4 fingerprints, and a single instance requires approximately 1 GB of RAM to run.
SureChEMBL’s FPSim2 file is not currently available for download, but we are considering generating it periodicaly and have created it once for you to try in Google Colab!

For substructure searches, we now also use an RDKit-based solution via SubstructLibrary, which returns results several times faster than our previous implementation. Additionally, structure search results are now sorted by molecule size, bringing the most relevant results to the top.

Structure depictions are now generated with RDKit, better aligning SureChEMBL with other services provided by our team.


What’s Next?

This is the first time we’ve integrated RDKit into SureChEMBL, and we're excited to explore further enhancements using our favourite toolkit. After this and the introduction of the query assistant, stay tuned for more updates!
 

 

Substructure search results for CNC(=O)C1=CC(OC2=CC=C(NC(=O)NC3=CC=CC=C3)C=C2)=CC=N1

 

 

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