BunkerFold-3: Protein Structure Prediction from Sequence

BunkerFold-3 is a 1.2B parameter protein structure prediction model. Given an amino acid sequence, it returns full 3D atomic coordinates with side chains, per-residue confidence scores, and a predicted fold class.

At a glance

Field	Value
Category	Protein
Parameters	1.2B
Version	v3.1
Endpoint	`POST /v1/models/bunkerfold-3/predict`
Typical latency	~2 seconds for sequences under 150 residues

Install

pip install bunker-fold

See Installation for full setup, including uv and poetry.

When to use

Predict structure for a novel sequence with no known homolog.
Resolve side-chain conformations for docking studies.
Screen designs from a protein engineering pipeline before wet-lab validation.

Example

curl -X POST https://api.bunkerbio.com/v1/models/bunkerfold-3/predict \
  -H "Authorization: Bearer $BUNKER_API_KEY" \
  -H "Content-Type: application/json" \
  -d '{
    "sequence": "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH"
  }'

import requests, os

r = requests.post(
    "https://api.bunkerbio.com/v1/models/bunkerfold-3/predict",
    headers={"Authorization": f"Bearer {os.environ['BUNKER_API_KEY']}"},
    json={"sequence": "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH"},
)
print(r.json())

Response

{
  "confidence": 0.97,
  "rmsd": 0.42,
  "residues_resolved": "51/51",
  "fold_class": "globin",
  "time_seconds": 1.8,
  "structure_url": "https://cdn.bunkerbio.com/predictions/abc123.pdb"
}

Parameters

string

required

Amino acid sequence in single-letter IUPAC codes. Maximum length 2,048 residues.

boolean

default:"true"

Include side-chain atoms in the returned structure.

string[]

Optional list of PDB IDs to use as templates. Leave empty for template-free prediction.

Response fields

number

Model-wide confidence score between 0 and 1.

number

Estimated RMSD in angstroms against the predicted best template.

string

Fraction of residues resolved at atomic detail, formatted as resolved/total.

string

Predicted structural class (for example, globin, immunoglobulin, tim_barrel).

string

Signed URL to a PDB file with the full predicted structure. Valid for 24 hours.

Get Started

Models

API Reference

Installation

BunkerFold-3: Protein Structure Prediction from Sequence

At a glance

Install

When to use

Example

Parameters

Response fields

​At a glance

​Install

​When to use

​Example

​Parameters

​Response fields

At a glance

Install

When to use

Example

Parameters

Response fields