boltz
Structure prediction for protein, nucleic-acid, and small-molecule complexes with Boltz-2 (Passaro & Wohlwend et al. 2025, github.com/jwohlwend/boltz). Reach for this skill to validate designed binders against a target, to co-fold a protein with a SMILES or CCD ligand, or to get an open-source Alpha
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- Лиценз
- Apache-2.0
- Последна проверка на записа
- 21.09.2026 г.
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Boltz-2
Boltz-2 is the open-weights diffusion co-folder closest in surface to
AlphaFold3: a YAML describing protein, DNA, RNA, and ligand chains in, mmCIF
plus pTM/ipTM/pLDDT confidences out, with an optional small-molecule affinity
head. Among our four co-fold skills it is the default for binder-validation
campaigns — fully open MIT weights and the fastest sampler; pick chai1 when
you want a second independent model for consensus, openfold3 when AF3-faithful
settings matter, and esmfold2 when you can live without an MSA. Code and
weights are MIT (PyPI boltz, github.com/jwohlwend/boltz).
Running it
# complex.yaml
version: 1
sequences:
- protein:
id: A
sequence: MVTPEGNVSLVDESLLVGVTDEDRAVRS... # target
- protein:
id: B
sequence: AIQRTPKIQVYSRHPAENG... # binder
- ligand:
id: L
smiles: 'N[C@@H](Cc1ccc(O)cc1)C(=O)O' # or ccd: SAH
boltz predict complex.yaml \
--use_msa_server --out_dir out/ --recycling_steps 3 --diffusion_samples 5
Each protein chain needs an MSA; without one the run exits before the model
loads. --use_msa_server queries api.colabfold.com (expect a 30–90 s pause
per chain) and is the right default unless you already have an .a3m to name
under msa: in the YAML. Setting msa: empty forces single-sequence mode —
that is an accuracy sacrifice, not a speed or memory optimization, because the
MSA search runs on CPU before the GPU stage starts.
Per input the output lands at out/boltz_results_complex/predictions/complex/.
Read confidence_complex_model_0.json first: iptm > 0.5 is the community
pass line for an interface, complex_plddt > 0.7 for the fold itself, and
confidence_score is the weighted aggregate the structures are ranked by.
Structures themselves are complex_model_{0..N-1}.cif (or .pdb with
--output_format pdb).
Affinity head
Add a properties: block naming one ligand chain as the binder and Boltz-2
predicts protein–small-molecule binding affinity alongside the structure:
properties:
- affinity:
binder: L # the ligand chain id, not the protein