AI-Powered Drug Discovery

Accelerated Molecular Discovery at Trillion Scale

Search, predict, and explore 2D, 3D shape, electrostatic, and activity similarity across 40T+ molecules in seconds — on cloud or on-prem.

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Read the 147× hit-rate case study

40T+

Molecules

Search Time

95%+

DFT Correlation

Database Partners

Ligand for PGK2 protein identified using CHEESE.

Trusted by leading organizations in drug discovery

The CHEESE Platform

A family of AI products for drug discovery that accelerate the early phases of your research

CHEESE Search

Single Second Search in Billion scale enumerated libraries (40B+ molecules). 3D Shape, Electrostatics & Activity Screening.

Aurigene, Enamine, ZINC, eMolecules
Chemspace, Otava/Chemriya, Mcule, Molport
Super friendly UI, advanced API

Search Molecules

CHEESE SynthonGPT

Trillion Scale (synthon-based) Search across 40T+ molecules. Fully adaptive metrics.

eMolecules, SynpleChem, Xtalpi, Enamine-public
Substructure and Superstructure Search
Molecular pattern filtering (200+ filters)

Search Molecules

CHEESE Navigator

Navigate the combinatorial spaces by acceleration of multi-property optimisation based, e.g. by docking, ligand-protein complex scoring (Boltz2).

40x faster than existing samplers
Adjust hit mining vs. scaffold explorations
Reach to complementary parts of the space vs. existing tools

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Deploy CHEESE your way

Private by design, built to integrate, and shaped to your workflows—from the cloud to fully on-premises behind your firewall.

On-Premises Privacy

Run CHEESE entirely behind your firewall. Your structures, queries, and IP never leave your infrastructure—maximum protection for confidential drug discovery programs.

Fully on-prem deployment
No data leaves your network
Maximum IP protection

Breadth of Integrations

Connect CHEESE to the tools your chemists already use. Public API plus native access from the command line, Python, and KNIME.

Public API & CLI
Python & KNIME integrations
Fits your existing stack

Wide Customisation

Tailor CHEESE to your pipeline. Index your own custom databases and integrate the platform directly into your existing discovery workflows.

Custom databases
Integration into existing workflows
Personalised deployment

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What Our Partners Say

"Collaboration with Deep MedChem has significantly streamlined the implementation of AI/ML technologies for processing chemoinformatics data in our drug discovery processes. Through a series of open consultations, the members of Deep MedChem quickly and effectively understood our needs. As a result of this collaboration, we now possess several proprietary models that provide us with significant competitive advantage over other solutions."

Jan Skácel

Research Group Lead, IOCB Prague

"CHEESE Modeller has been a game-changer for our drug discovery projects. The tool accurately predicted docking scores in our virtual screening saving us 200 days of computation time, while achieving unprecedented hit rate. Its simplicity and ease of use set it apart from competitors. Their customer support is outstanding, always providing prompt and effective assistance."

Chief Scientific Officer

A San Francisco Bay Area Biotech Company

AI is revolutionising drug discovery. We will make you part of this revolution.

Deep MedChem is a spin-off from The MAMA AI and i&i Prague—a startup investor and incubator connected with IOCB, a top-class medicinal chemistry institution in Europe.

The collaboration led to the development of CHEESE platform—a family of AI products for drug discovery that accelerate the early phases of drug discovery.

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