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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 for free (GUI) and after user self-registration (APIs) at

Contact us at We are ready to take your inquiries. Also we are always interested in your feedback and suggestions.


CHEESE Talk in Miton AI Talks series (March, 2024)

Our CTO Miroslav Lžičař gave a talk in the Miton AI times series on how we make billion- and trillion-scale molecular spaces accessible for search and filtering by properties. You can watch the recording on YouTube:

CHEESE Modeller is available for customers! (February, 2024)

Build your custom fast predictive models for molecular properties with CHEESE Modeller with state of the art prediction performance.

Key benefits of CHEESE Modeller: speed of training of the predictive models, the speed of prediction by the models, very good performance of the predictive models (state of the art in most cases of ADMET properties), ability to train the models on your own data and (optionally) on your dedicated instance (or even on AWS or on premises on your own servers). Contact us!

On-Premise Version of CHEESE Search Now Available! (January, 2024)

Due to popular demand our team has dedicated substantial efforts to bring you the on-premise version of CHEESE Search! We understand that many customers prioritise the security of their sensitive data and prefer not to transmit it over the internet. With the introduction of the OnPrem CHEESE, you can now experience all the incredible benefits of CHEESE while maintaining the confidentiality of your data. Discover more details in our documentation section titled "OnPrem CHEESE."

Deep MedChem will comercialize CHEESE family of products (December, 2023)

We are thrilled to announce the establishment of Deep MedChem, a cutting-edge company dedicated to commercialise the CHEESE family of products---advanced molecular search tools and their extensions to the market. Founded in the first half of December, Deep MedChem is committed to revolutionising the landscape of drug development AI tools and their accessibility.

CHEESE Webinar with ChemSpace (August 10, 2023)

We had the pleasure to present details of CHEESE in the webinar series of ChemSpace.

Presentation slides from the webinar:

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)

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