BunkerFold-3: Protein Structure Prediction from Sequence
BunkerFold-3 predicts 3D protein structure from an amino acid sequence with sub-angstrom accuracy on CASP15 targets and full side-chain resolution.
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.
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.
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