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CHEESE - An AI-based Super Fast Search in Molecular Space

The ability to rapidly search and analyze large databases of molecules for similar compounds will revolutionize drug discovery and chemical informatics. Searching large databases using traditional means is, however, extremely slow and therefore intractable.

To address these challenges, we developed a new fast and scalable tool: CHEESE (Chemical Embeddings Search Engine) for searching fast very large chemical spaces. The CHEESE tool learns representation of the molecular space that is then the core of molecule similarity search. The representation has the ability to be trained on many molecular similarity metrics (2D, 3D, electrostatic). Furthermore, the learned molecule representations can be leveraged for multiple downstream tasks such as molecular property prediction.

The CHEESE tool is available after user self-registration online at

Contact us at We are interested in your feedback and suggestions, we are also open to collaboration.


CHEESE Webinar with ChemSpace (August 10, 2023)

We had the pleasure to present details of CHEESE in the webinar series of ChemSpace. Here is the recording:

New Content on CHEESE-DOCS (July 27, 2023)

  • Look on Prototypes page to see what we are working on. And Benchmarks page to see how CHEESE performs in various tasks. Changelog page contains information about new features in each version of CHEESE webpage and features of upcoming versions.

CHEESE was presented at the BioML Conference (July 17, 2023)

You can scroll through the slides

CHEESE was presented at the BioVaria conference (April 29-30, 2023)

You can scroll through the slides