RFdiffusion3 — Enzyme design examples

RFD3 contains several knobs and dials for enzyme design.

  • input: the pdb or cif file that contains the input theozyme

  • ligand: any ligand res names that are to be included (comma separated)

  • unindex: which residues should have their index be inferred by the model instead of prespecified

  • length: the length range of the generated protein

  • select_fixed_atoms: dictionary that indicated which atoms should be fixed (can use ALL, BKBN, or TIP for all atoms in the residue, backbone atoms only and tip atoms only)

If you would like to run the examples below, enzyme_design.json, located in this directory, contains the example code. You can run it via:

rfd3 design out_dir=inference_outputs/enzyme/0 \
ckpt_path=/path/to/rfd3_foundry_2025_12_01.ckpt \
inputs=./enzyme_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/enzyme/0 \
ckpt_path=/path/to/rfd3_foundry_2025_12_01.ckpt \
inputs=./enzyme_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.

{
    "M0255_1mg5_unfixed": {
        "input": "./input_pdbs/M0255_1mg5.pdb", 
        "ligand": "NAI,ACT",
        "unindex": "A108,A139,A152,A156",
        "length": "180-200",
        "select_fixed_atoms": {
            "A108": "ND2,CG",
            "A139": "OG,CB,CA",
            "A152": "OH,CZ",
            "A156": "NZ,CE,CD",
            "ACT": "OXT",
            "NAI": ""
        }
    }
}