boltz-protein-screen

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.

1. 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.
2. 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.
3. Don't add bonds / constraints unless the user asks for geometry constraints.