# RFdiffusion3 — Protein binder design examples
RFD3 is a highly proficient protein binder designer. The following arguments have to be specified to RFD3 to make protein binders.
- input: the PDB or CIF file of the structure you want to bind
- contig: the length range of the binder to make (indicated as a range) and which residues from the target file to consider. 
- infer_ori_strategy: how RFD3 decides to place the origin of the generated protein binder with respect to the target. We find that using the "hotspots" strategy works best
- select_hotspots: which atoms on the target should be bound (dictionary of residues on the target and atoms in those residues)

In addition, we strongly recommend the following setting, which encourages the model to make more structured designs:
- is_non_loopy: true

Some useful command-line overrides to experiment with include `inference_sampler.step_scale` (defaults to 1.5) and
`inference_sampler.gamma_0` (defaults to 0.6). Increasing the `step_scale` and decreasing `gamma_0` yields lower-temperature
designs, which tends to increase designability and decrease diversity.

If you would like to run the examples below, `protein_binder_design.json`, located in this directory, contains the example code. You can run it via:
```
rfd3 design out_dir=inference_outputs/protein_binder/0 \
ckpt_path=/path/to/rfd3_foundry_2025_12_01.ckpt \
inputs=./protein_binder_design.json
```

Or, if you have cloned the repo rather than using `pip install`:
```
python path/to/foundry/models/rfd3/src/rfd3/run_inference.py \
out_dir=inference_outputs/protein_binder/0 \
ckpt_path=/path/to/rfd3_foundry_2025_12_01.ckpt \
inputs=./protein_binder_design.json 
```

An example script for running these examples in batches is also provided in `run_inf_tutorial.sh`.

The input files for the different examples are provided in `foundry/models/rfd3/docs/input_pdbs`.

```json
{
    "insulinr": {
        "dialect": 2,
        "infer_ori_strategy": "hotspots",
        "input": "input_pdbs/4zxb_cropped.pdb",
        "contig": "40-120,/0,E6-155",
        "select_hotspots": {
            "E64": "CD2,CZ",
            "E88": "CG,CZ",
            "E96": "CD1,CZ",
            },
        "is_non_loopy": true
    },
    "pdl1": {
        "dialect": 2,
        "infer_ori_strategy": "hotspots",
        "input": "input_pdbs/5o45_cropped.pdb",
        "contig": "50-120,/0,A17-131",
        "select_hotspots": {
            "A56": "CG,OH",
            "A115": "CG,SD",
            "A123": "CD2,OH",
       },
        "is_non_loopy": true
    }
}
```