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Raktim Mitra
2026-03-28 12:04:48 -07:00
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models/rfd3/README.md
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# De novo Design of Biomolecular Interactions with RFdiffusion3
RFdiffusion3 (RFD3) is a diffusion method that can design protein structures
RFdiffusion3 (RFD3) is a diffusion method that can design biopolymer structures
under complex constraints.
This repository contains both the training and inference code, and
@@ -62,6 +62,8 @@ For example, you can fix sequence and not structure (prediction-type task), fix
For full details on how to specify inputs, see the [input specification documentation](./docs/input.md). You can also see `foundry/models/rfd3/configs/inference_engine/rfdiffusion3.yaml` for even more options.
Nucleic acid design, along with proteins, is also possible using RFD3 using the atom23 checkpoints. For full details see the [atom23 design documentation](./docs/examples/atom23_design.md)
## Further example JSONs for different applications
Additional examples are broken up by use case. If you have cloned the
repository, matching `.json` files are in `foundry/models/rfd3/docs/examples`
@@ -75,30 +77,30 @@ you will need to change the path in the `.json` file(s) before running.
<table>
<tr>
<td align="center">
<h3><a href="./docs/sm_binder_design.md">Small molecule binder design</a></h3>
<h3><a href="./docs/examples/sm_binder_design.md">Small molecule binder design</a></h3>
<img src="docs/.assets/sm.png" height="150" />
</td>
<td align="center">
<h3><a href="./docs/protein_binder_design.md">Protein binder design</a></h3>
<h3><a href="./docs/examples/protein_binder_design.md">Protein binder design</a></h3>
<img src="docs/.assets/ppi.png" height="150" />
</td>
<td align="center">
<h3><a href="./docs/na_binder_design.md">Nucleic acid binder design</a></h3>
<h3><a href="./docs/examples/na_binder_design.md">Nucleic acid binder design</a></h3>
<img src="docs/.assets/dna.png" height="150" />
</td>
</tr>
<tr>
<td align="center">
<h3><a href="./docs/enzyme_design.md">Enzyme design</a></h3>
<h3><a href="./docs/examples/enzyme_design.md">Enzyme design</a></h3>
<img src="docs/.assets/enzyme.png" height="150" />
</td>
<td align="center">
<h3><a href="./docs/symmetry.md">Symmetric design</a></h3>
<h3><a href="./docs/examples/symmetry.md">Symmetric design</a></h3>
<img src="docs/.assets/symm.png" height="150" />
</td>
<td align="center">
<h3><a href="./docs/multipolymer.md">Multipolymer design</a></h3>
<h3><a href="./docs/examples/atom23_design.md">Multipolymer design</a></h3>
<img src="docs/.assets/multipolymer.png" height="150" />
</td>

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models/rfd3/docs/examples/atom23_design.md
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}
}
```
### Note: Most of the above jsons is not actually reading the `input` field. Kept as a dummy for the `inference3_engine`.
### Note: Most of the above jsons is not actually reading the `input` field. Kept as a dummy for the `inference_engine`.
## 4. Ligand-Conditioned Aptamer Design