FreeBindCraft

Overview

Exploring binder candidates against a target surface.
Running focused or broader binder-design searches with target residue hints.
Generating candidate structures for downstream sequence design, prediction, and filtering.

Modes

Mode	Input shape	When to use it
`miniprotein_binder` Miniprotein Binder Default	Uses one selected file/source when file parameters are present.	Design 31+ residue protein binders against a target PDB.
`peptide_binder` Peptide Binder	Uses one selected file/source when file parameters are present.	Design short 8-30 residue peptide binders against a target PDB.

Canonical Job Configuration

These are the fields exposed by the default job configuration for freebindcraft. They are also returned by GET /api/v1/program/params?program=freebindcraft and submitted as the params JSON object to POST /api/v1/job/submit.

Parameter	Type	Modes	What it does
`target_structure` Target Structure	Structure file	All modes	Choose the target PDB from an upload, dataset, or previous job output. Required; Files: .pdb
`binder_name` Binder Name	Text	All modes	Prefix used for designed binder files. Required
`target_chains` Target Chains	Text	All modes	Target chain IDs to keep from the PDB; other chains are ignored. Required; Default: A
`hotspot_residues` Hotspot Residues	Residue selection	All modes	Optional focused binding site. Leave blank to let FreeBindCraft choose.
`miniprotein_min_length` Min Length	Integer	Miniprotein Binder	Minimum binder length for miniprotein designs. Required; Default: 65; Range: 31-300
`miniprotein_max_length` Max Length	Integer	Miniprotein Binder	Maximum binder length for miniprotein designs. Required; Default: 150; Range: 31-300
`peptide_min_length` Min Length	Integer	Peptide Binder	Minimum peptide length. Required; Default: 8; Range: 8-30
`peptide_max_length` Max Length	Integer	Peptide Binder	Maximum peptide length. Required; Default: 25; Range: 8-30
`final_designs` Final Designs	Integer	All modes	Number of filter-passing binders to collect before stopping. The job form also applies a finite trajectory budget; use advanced args for very large campaigns. Default: 100; Range: 1-200
`miniprotein_profile` Design Profile	Text	Miniprotein Binder	Choose the main design strategy preset. Default: Standard; Options: Standard, Flexible target, Hard target, Beta-sheet bias
`peptide_profile` Design Profile	Text	Peptide Binder	Choose the main design strategy preset. Default: Standard; Options: Standard, Flexible target
`filter_strictness` Filter Strictness	Text	All modes	Standard filters are recommended; relaxed or off can help exploratory runs. Default: Standard; Options: Standard, Relaxed, No filters

Advanced configuration fields

Parameter	Type	Modes	What it does
`ranking_metric` Rank Final Designs By	Text	All modes	Rank accepted designs by interface predicted TM-score or interface predicted Structural Alignment Error. Default: i_pTM; Options: i_pTM, ipSAE
`redesign_interface` Redesign Interface	Yes/no	All modes	Allow ProteinMPNN to redesign interface residues instead of fixing them. Default: false
`save_plots` Save Plots	Yes/no	All modes	Save trajectory plots in the outputs. Default: true
`save_animations` Save Animations	Yes/no	All modes	Animations can make outputs much larger. Default: false
`verbose_logs` Verbose Logs	Yes/no	All modes	Enable detailed FreeBindCraft timing and progress logs. Default: false

Outputs And Metrics

Candidate binder structures and design metadata.
Score or ranking tables when produced by the selected protocol.
Treat ranking and confidence values as prioritization signals. Inspect interfaces and validate with independent prediction before experiments.

Common Examples

Focused epitope binder search using a target structure, selected target chain, and hotspot residues.
Broad binder exploration with a length range and a modest number of final candidates.

Example API params

{
  "mode": "miniprotein_binder",
  "target_structure": "target.pdb",
  "binder_name": "target_binder",
  "target_chains": "A",
  "hotspot_residues": "A45,A52,A76",
  "miniprotein_min_length": 70,
  "miniprotein_max_length": 120
}

Caveats

Binder design is stochastic and hit rate depends strongly on target preparation and epitope choice.
Residue numbering and chain IDs must match the uploaded target file.
Generated candidates require downstream validation and experimental testing.

Advanced Submit

Advanced submit is still available for direct program arguments through POST /api/v1/job/submit-advanced. Prefer canonical configuration unless you need exact low-level arguments or are reproducing a known command line.

Advanced submit exposes lower-level FreeBindCraft protocol arguments for users reproducing a known run setup.
Use canonical configuration for normal target, epitope, and design-count settings.

curl -X POST https://subseq.bio/api/v1/job/submit \
  -H "Authorization: Bearer <api_key>" \
  -F program=freebindcraft \
  -F 'params={"mode":"binder_design","target_structure":"target.pdb","target_chains":"A","hotspots":"A45,A52,A76","binder_length":"70-120"}'