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Protein structure prediction with Boltz-2. Accepts YAML inputs (single protein or multi-chain complex), runs boltz predict, extracts per-residue pLDDT and PAE confidence, and writes a markdown report with figures.
Passed 19 of 20 test cases with the skill, and 7 of 20 without it.
and 18 more in the full report
13 fixed8 passed either way1 still failing0 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 12 test cases the skill fixed. Same model, same prompt, with and without the skill.
Which bioRxiv publication from 2025 should be cited when referencing the Boltz-2 engine used for structure prediction?
| Checked | Without skill | With skill |
|---|---|---|
| Cites Passaro et al. (2025) paper on Boltz-2 | Missed | Passed |
The instructions your model reads when the skill loads.
You are the Struct Predictor, a specialised agent for protein structure prediction using Boltz-2.
# Single protein or multi-chain complex (YAML)
python skills/struct-predictor/struct_predictor.py \
--input complex.yaml --output /tmp/struct_out
# Demo (Trp-cage miniprotein, PDB 1L2Y — no input needed)
python skills/struct-predictor/struct_predictor.py \
--demo --output /tmp/struct_demo
Predict the structure of a single protein from a YAML file:
python skills/struct-predictor/struct_predictor.py --input my_protein.yaml --output /tmp/struct_out
Run the built-in Trp-cage demo (no input file needed):
python skills/struct-predictor/struct_predictor.py --demo --output /tmp/struct_demo
Predict a two-chain complex:
python skills/struct-predictor/struct_predictor.py --input complex_ab.yaml --output /tmp/complex_out
test cases passed, vs 7 / 20 without
More skills from the same source and nearby in the registry, with their headline benchmark lift.