| name | boltz-protein-screen |
| description | Screen existing protein binders with Boltz. Use when ranking a supplied protein, peptide, antibody, nanobody, or binder library against a target. Not for designing new proteins or screening small molecules. |
Workflow
If boltz-api is missing from PATH, use boltz-cli-setup for install/update guidance before retrying.
If a command reports missing or expired authentication, use boltz-cli-setup to start boltz-api auth login --device-code before retrying; do not ask permission first.
If the agent host sandbox blocks boltz-api install/auth/API calls, use boltz-cli-setup to request the host sandbox bypass/escalation needed for user-wide CLI install, browser login, credential storage, temp files, or API access before retrying.
Use this skill when the user already has candidate proteins / peptides / antibodies / nanobodies.
- Normalize the binder library into
proteins — a list of candidate complexes. For a simple sequence library each entry has one protein entity; multi-chain candidates (antibody heavy+light) are also allowed.
- Pick the target variant:
structure_template — user has a CIF/PDB file or URL; select which chains are polymer vs ligand, which residues to keep (crop_residues), and optionally epitope_residues / flexible_residues.no_template — user has only sequences; pass them as target.entities plus optional epitope_residues.
- Don't add
bonds / constraints unless the user asks for geometry constraints.
- Author the payload YAML or JSON, run
estimate-cost, show the USD cost, wait for explicit confirmation.
