RFdiffusion3
Baker Lab / IPD (University of Washington)
Third-generation diffusion model for protein design unifying backbone generation, sequence design, and all-atom refinement. Open-sourced Dec 2025 with full training code.
Best For
State-of-the-art unified protein design; supersedes RFdiffusion and RFdiffusion2
License
Open Source (check repo)
Strengths
- +Unified backbone + sequence + all-atom
- +Full training code released
- +Broader design space than predecessors
Limitations
- −Very new (Dec 2025)
- −Significant GPU requirements
- −Community adoption still early
R&D Pipeline Coverage
Related Tools
RFdiffusion
Baker Lab / IPD (University of Washington)
Diffusion-based generative model for de novo protein backbone design. Generates novel protein structures conditioned on binding targets, symmetry, or functional sites.
RFdiffusion All-Atom
Baker Lab / IPD (University of Washington)
Extension of RFdiffusion that jointly diffuses over protein backbone AND small molecule ligands, enabling de novo design of proteins that bind specific small molecules like heme or digoxigenin.
ProteinMPNN
Baker Lab / IPD (University of Washington)
Inverse folding model: generates amino acid sequences predicted to fold into a target 3D backbone structure. Standard component of all modern protein design pipelines.
More in Generative Design
RFdiffusion
Baker Lab / IPD (University of Washington)
Diffusion-based generative model for de novo protein backbone design. Generates novel protein structures conditioned on binding targets, symmetry, or functional sites.
RFdiffusion2
Baker Lab / IPD (University of Washington)
Successor to RFdiffusion using flow matching. Designs enzymes directly from active site geometry (theozyme) specifications.
ProteinMPNN
Baker Lab / IPD (University of Washington)
Inverse folding model: generates amino acid sequences predicted to fold into a target 3D backbone structure. Standard component of all modern protein design pipelines.
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