RFdiffusion2 vs RFdiffusion3

RFdiffusion2: Atom-level enzyme active-site scaffolding with diffusion, no sequence-position constraints. RFdiffusion3: All-atom diffusion model from the Baker lab for designing protein binders to DNA, proteins and small molecules, plus enzymes; ~10x faster than RFdiffusion2.

Facts below come from each project's own website, repository and paper. We don't publish benchmark claims here; see the papers for evaluations. Shared tags: diffusion, all-atom.

FieldRFdiffusion2RFdiffusion3
TaskEnzyme active-site scaffoldingAll-atom protein design
ModalitiesEnzyme from functional-group geometryAll-atom protein design; nucleic-acid design via extension
MSA required——
Open weightsYesYes (foundry install base-models)
GPU need—CUDA GPU; inference also on Apple Silicon MPS
LicenseBSD-3-ClauseBSD-3-Clause
PricingOpen sourceOpen source
Released2025-04-102025-09-18
PaperLinkLink
GitHubGitHubGitHub
GitHub stars4501,003
Interface—Package (foundry)

License and commercial use

FieldRFdiffusion2RFdiffusion3
Code licenseBSD-3-ClauseBSD-3-Clause
Weights license——
Commercial usePermissive (commercial OK)Permissive (commercial OK)
AnswerYes. The recorded license is permissive, so closed-source commercial use is allowed if you keep the notices. DetailsYes. The recorded license is permissive, so closed-source commercial use is allowed if you keep the notices. Details

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