Chemistry & ADMET · Correia Lab / EPFL
DiffSBDD
Equivariant diffusion that generates molecules inside a given binding pocket.
What DiffSBDD is
DiffSBDD generates 3D molecules conditioned on a protein pocket rather than sampling from chemical space and docking afterwards, so the geometry it produces is already in the site. The released checkpoints cover two training sets and two conditioning schemes, in both a full-atom and a C-alpha pocket representation, which is the choice that trades resolution against speed. Beyond de novo generation it supports substructure inpainting — fixing fragments and growing the rest, which covers scaffold elaboration and fragment linking — and an evolutionary optimisation loop that repeatedly noises and denoises a population against drug-likeness or synthetic accessibility. Code is MIT; the checkpoints are published separately and carry their own licence.
Run it here
We list this model but cannot run it yet: its checkpoints are published on Zenodo rather than a model hub, so a GPU image has to fetch and pin them — we have not built one yet.
Everything on this page still applies. Running it needs a loader for this repository, not a bigger machine.
Inputs and outputs
You provide
Pocket structure (PDB)
The pocket is defined by a reference ligand in the file, or by a list of residues.
Reference ligandoptional
Chain and residue of a ligand already in the structure, used to locate the pocket.
Moleculesoptional
You get back
3D molecules placed in the pocket, as an SDF file.
Licence
Commercial use permitted · MIT code / CC BY 4.0 weights
Verified 2026-10-24: the repository declares MIT, and the Zenodo record holding the eight released checkpoints declares CC BY 4.0 — commercial use permitted, attribution required. The two licences are separate documents and both have to be honoured.
Questions
Can I use DiffSBDD commercially?
Commercial use permitted. Verified 2026-10-24: the repository declares MIT, and the Zenodo record holding the eight released checkpoints declares CC BY 4.0 — commercial use permitted, attribution required. The two licences are separate documents and both have to be honoured.