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.
Best For
Designing proteins that bind specific small molecules; co-designing protein-ligand complexes
License
Open Source (MIT)
Strengths
- +Joint protein + small molecule diffusion
- +Experimentally validated binders
- +MIT license
Limitations
- −Requires RoseTTAFold All-Atom for structure prediction
- −Limited to small molecule ligands
- −Computationally intensive
R&D Pipeline Coverage
Related Tools
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ProteinMPNN
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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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