FreeBindCraft

De novo binder design with AlphaFold2 backprop, ProteinMPNN, and open-source scoring.

Inputs

Upload your target structure (PDB) and JSON configs under /inputs.
--settings is required; relative paths are normalized into /inputs.
--filters and --advanced are optional; include them to override the upstream defaults.
--no-pyrosetta is enforced automatically for open-source scoring.

Quick-start args

--settings=/inputs/settings.json
--filters=/inputs/filters.json
--advanced=/inputs/advanced.json

Swap the JSON paths for your files; relative paths are fine.

Example config files

These are minimal, copy/pasteable examples that match the container filesystem: inputs under /inputs and outputs under /outputs.

settings.json (required)

{
  "design_path": "/outputs/my_freebindcraft_run",
  "binder_name": "binder",
  "starting_pdb": "/inputs/target.pdb",
  "chains": ["A"],
  "target_hotspot_residues": ["56"],
  "lengths": [65, 90],
  "number_of_final_designs": 25
}

filters.json (optional)

{
  "Average_pLDDT": { "threshold": 0.8, "higher": true },
  "Average_i_pTM": { "threshold": 0.6, "higher": true },
  "Interface_SASA_%": { "threshold": 0.2, "higher": true },
  "ShapeComplementarity": { "threshold": 0.55, "higher": true },
  "dG": { "threshold": -10.0, "higher": false }
}

advanced.json (optional)

{
  "design_algorithm": "4stage",
  "use_multimer_design": false,
  "num_recycles_design": 3,
  "num_recycles_validation": 1,
  "sample_models": true,
  "rm_template_seq_design": true,
  "omit_AAs": ["C", "M"],
  "force_reject_AA": false
}

Submit

Launch via New Job -> FreeBindCraft after uploading your inputs.