Protein Structure · IntelliGen AI
IntelliFold
Open-weight complex prediction across proteins, nucleic acids and ligands, Apache-2.0 throughout.
What IntelliFold is
IntelliFold predicts the structure of a biomolecular assembly — proteins with nucleic acids, ligands and modified residues — from sequence, in the same input format the AlphaFold 3 family uses. Its interest here is licensing as much as accuracy: the code and the published model parameters are both Apache-2.0, which is rare among the credible all-atom predictors and is what lets it be used in commercial work without a separate agreement. Version 2 runs on the Apache-2.0 release of AlphaFold 3's inference engine, which the project vendors; the AlphaFold 3 weights, which are non-commercial, are not part of it and are not used. An optional inference-time steering mode nudges the sampler toward physically valid ligand poses, which the authors report raises pose validity substantially on their own evaluation at a cost in run time.
Run it here
We list this model but cannot run it yet: it needs its own inference engine and a GPU image, which we have not built yet.
Everything on this page still applies. Running it needs a loader for this repository, not a bigger machine.
Inputs and outputs
You provide
Assembly definition
Chains and ligands that make up the complex. Alignments can be supplied with the input or searched for separately.
Structures to sampleoptional
Independent diffusion samples, ranked by the model's own confidence.
Physical steeringoptional
You get back
All-atom coordinates for the whole assembly.
Per-residue and per-interface confidence for the ranked prediction.
Licence
Commercial use permitted · Apache-2.0
Verified 2026-10-24: the repository's licence file, its model card and its own licence statement all declare Apache-2.0 for the code and for the released model parameters, with commercial use permitted. It vendors the Apache-2.0 release of AlphaFold 3 as its inference engine and ships none of AlphaFold 3's own weights, which carry separate non-commercial terms.
Questions
Can I use IntelliFold commercially?
Commercial use permitted. Verified 2026-10-24: the repository's licence file, its model card and its own licence statement all declare Apache-2.0 for the code and for the released model parameters, with commercial use permitted. It vendors the Apache-2.0 release of AlphaFold 3 as its inference engine and ships none of AlphaFold 3's own weights, which carry separate non-commercial terms.