Genie 3

Overview

Unconditional backbone generation from an exact length.
Scaffolding benchmark or custom motifs.
Binder design against bundled benchmark targets or custom target structures.

Modes

Mode	Input shape	When to use it
`unconditional_generation` Unconditional Generation Default	No uploaded input is required by the mode itself.	Generate de novo protein backbones from an exact length.
`motif_scaffolding` Motif Scaffolding	Uses one selected file/source when file parameters are present.	Scaffold a bundled benchmark motif or a Genie-compatible custom motif.
`binder_design` Binder Design	Uses one selected file/source when file parameters are present.	Design binders for a bundled benchmark target or a custom target structure.

Canonical Job Configuration

These are the fields exposed by the default job configuration for genie3. They are also returned by GET /api/v1/program/params?program=genie3 and submitted as the params JSON object to POST /api/v1/job/submit.

Parameter	Type	Modes	What it does
`samples` Samples	Integer	All modes	How many sequences or designs to sample. Default: 1; Range: 1-32
`length` Length	Integer	Unconditional Generation	Exact sequence length for unconditional generation. Default: 50; Range: 50-300
`motif_source` Motif Source	Text	Motif Scaffolding	Use the bundled benchmark or provide a Genie-compatible motif PDB plus segment layout. Default: bundled; Options: bundled, custom
`motif_selection` Motif Benchmark	Text	Motif Scaffolding	Bundled benchmark case for motif scaffolding. Default: 22_1BCF; Options: 22_1BCF; Shown when motif_source is bundled
`motif_structure` Motif PDB	Structure file	Motif Scaffolding	PDB containing REMARK 999 NAME and REMARK 999 INPUT segment lines, as expected by Genie 3. Required; Files: .pdb; Shown when motif_source is custom
`motif_layout` Segment Layout	Text	Motif Scaffolding	Comma-separated scaffold ranges and motif segment IDs from the motif PDB REMARK lines. Required; Shown when motif_source is custom
`binder_source` Target Source	Text	Binder Design	Use the bundled benchmark or provide a custom target PDB, sequence, and interface residues. Default: bundled; Options: bundled, custom
`binder_selection` Binder Benchmark	Text	Binder Design	Bundled benchmark case for binder design. Default: 01_bhrf1; Options: 01_bhrf1; Shown when binder_source is bundled
`target_structure` Target PDB	Structure file	Binder Design	Target structure for Genie 3 binder conditioning and template-mode evaluation. Required; Files: .pdb; Shown when binder_source is custom
`target_sequence` Target Sequence	Sequence	Binder Design	Target amino-acid sequence. Use colon-separated chains for multi-chain targets. Required; Shown when binder_source is custom
`target_segments` Target Segments	Residue selection	Binder Design	Target residue spans included in the binder-design context. Required; Shown when binder_source is custom
`hotspots` Hotspots	Residue selection	Binder Design	Target residues to condition the binder interface on. Required; Shown when binder_source is custom
`binder_length` Binder Length	Length or range	Binder Design	Length or length range for generated binder chains. Required; Range: 3-500; Shown when binder_source is custom
`folding_mode` Folding Mode	Text	Binder Design	Template mode uses the target PDB as the ColabFold template. MSA mode also requires a target MSA file. Default: template; Options: template, msa; Shown when binder_source is custom
`target_msa` Target MSA	MSA file	Binder Design	Target MSA used by Genie 3/ColabFold when folding mode is msa. Required; Files: .a3m, .afa, .sto, .stk, .fa, .fasta; Shown when folding_mode is msa

Advanced configuration fields

Parameter	Type	Modes	What it does
`total_length` Total Length	Length or range	Motif Scaffolding	Optional total scaffolded protein length or range. Leave blank to sample from the segment layout ranges. Range: 1-2000; Shown when motif_source is custom
`extended_interface` Extended Interface	Residue selection	Binder Design	Optional broader interface residue set. Genie 3 defaults generation conditioning to this key. Shown when binder_source is custom
`problem_name` Problem Name	Text	Motif Scaffolding, Binder Design	Optional short key for generated custom Genie 3 problem files.
`inverse_sequences` Inverse-Fold Sequences	Integer	Binder Design	ProteinMPNN sequences sampled per generated binder backbone during evaluation. Default: 1; Range: 1-8
`direction_scale` Direction Scale	Number	All modes	Optional sampler guidance strength. Leave blank for the workflow default. Range: 0-2
`experiment_name` Experiment Name	Text	All modes	Optional short name written into the generated Genie 3 config.

Outputs And Metrics

Generated backbone structures and associated metadata.
Result summaries for sampled designs when produced by the wrapper.
Use generated structures as candidates for sequence design, prediction, filtering, and manual structural inspection.

Common Examples

Unconditional generation: length 80, samples 8.
Motif scaffolding: bundled motif benchmark with optional total length range.
Binder design: custom target PDB, target sequence, interface residues, and sample count.

Example API params

{
  "mode": "unconditional_generation",
  "length": 80,
  "samples": 8
}

Caveats

Custom motif PDBs must use Genie-compatible REMARK lines and segment layout.
Binder interface residue lists must match the submitted target sequence/structure.
Backbones are proposals and need sequence design and independent validation.

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 can pass direct Genie configuration for custom campaigns.
Canonical configuration covers the common unconditional, motif, and binder modes.

curl -X POST https://subseq.bio/api/v1/job/submit \
  -H "Authorization: Bearer <api_key>" \
  -F program=genie3 \
  -F 'params={"mode":"unconditional_generation","length":80,"samples":8}'