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 geometric steering.
4. Author the payload YAML or JSON, run estimate-cost, show the USD cost, wait for explicit confirmation.
5. start to submit. Capture the ID.
6. Launch download-results with the agent runtime's background/non-blocking command facility. In Claude Code, use Bash with run_in_background: true. In Codex, run download-results as a foreground shell command with yield_time_ms: 1000; if Codex returns a session_id, keep it for optional later polling. After launching it, report the job ID, run name, and output directory, then end the turn immediately. Do not wait on the background session unless the user explicitly asks for progress.
7. Rank hits from <output-root>/<run-name>/results/index.jsonl by binding_confidence descending. Use iptm and min_interaction_pae as tiebreakers. optimization_score is not emitted for this endpoint. Read references/results.md for output layout and metric details.

Command Pattern

# Replace placeholders with concrete absolute paths before running.
# Use a short descriptive run name, for example: protein-screen-<target>-<library>-v1

boltz-api protein:library-screen estimate-cost \
  --input @yaml:///absolute/path/payload.yaml

boltz-api protein:library-screen start \
       --idempotency-key "<run-name>" \
       --input @yaml:///absolute/path/payload.yaml \
       --raw-output --transform id

# Copy the printed job ID into this command, then launch it in the agent
# runtime's background/non-blocking mode.
# Claude Code: Bash with run_in_background=true.
# Codex: foreground shell command with yield_time_ms=1000; keep the returned session_id if one is provided.
# Do not append "&" or use nohup in Codex.
boltz-api download-results \
  --id "<job-id-from-start>" --name "<run-name>" \
  --root-dir "/absolute/path/boltz-experiments" \
  --poll-interval-seconds 30

Payload keys are proteins, target — API body field names.

Always Do This

• For structure_template, embed CIF/PDB bytes with @data:///abs/path/target.cif inside the structure.data field. Don't use bare @path (the auto-sniff once sent CIF as plain text into a base64 field and broke the server parser).
• Residue indices are 0-based. epitope_residues and flexible_residues must be subsets of crop_residues.
• Keep payload field names exactly as the API body names shown in references/api.md.
• Use absolute paths for the output root, payload files, and embedded target files. Do not cd into the run directory for follow-up commands; pass the same --root-dir and use absolute paths so later relative paths do not drift.
• Prefer one merged top-level payload via --input @yaml:///absolute/path/payload.yaml or @json:///absolute/path/payload.json for estimate-cost and start. Keep --idempotency-key and --workspace-id top-level; if they also appear inside --input, the top-level flags win.
• Direct object flags still work as overrides, such as --target @yaml:///absolute/path/target.yaml or repeated --protein @json:///absolute/path/protein-1.json entries. Piped YAML / JSON on stdin also works, but it must use API body field names. Never use @file:// or @./.
• Use the same slug as both --idempotency-key and --name.
• In permission-gated agents such as Claude Code, keep each Boltz call as a top-level command that starts with boltz-api. Prefer concrete arguments over sh -c, inline environment assignments, aliases, wrapper scripts, loops, or pipelines around the boltz-api invocation unless the user already allowed that exact command form. Use --raw-output --transform id, read the printed ID, then paste that literal ID into the next download-results command.
• Prefer the agent runtime's background/non-blocking command mode for download-results. In Codex specifically, keep download-results in the foreground and set the shell tool yield to 1000 ms; Codex will return a session_id if the command is still running. Do not append & or use nohup in Codex because the tool runner may clean up shell-backgrounded descendants before .boltz-run.json is fully written.
• After the background/session starts, do not wait on it or poll it. --poll-interval-seconds 30 is a reasonable default. download-results emits JSONL progress on stderr by default; add --progress-format text --verbose only when you explicitly want human-readable logs. Report the job ID, run name, output directory, and that the runtime should notify when the background command completes.
• Only check status when the user asks. In Codex, poll the saved session with an empty write_stdin, or prefer boltz-api --format json download-status --name "<run-name>" --root-dir "/absolute/path/boltz-experiments" for structured local checkpoint state. Never run a manual poll loop.
• If detached download needs to be restarted, re-run boltz-api download-results with the same --name "<run-name>" and the same --root-dir.
• Cost scales with total complex length (target + candidate). Typically ≈$0.025 per submitted candidate for small complexes, more for larger ones. Quote the exact figure from estimate-cost.

Escape Hatch

• Payload reference: https://api.boltz.bio/docs/api/python/resources/protein/subresources/library_screen/methods/start
• CLI flag names: boltz-api protein:library-screen start --help

Read references/api.md for the proteins list shape and both target variants (structure_template with chain_selection, and no_template with epitope hints). Read references/results.md after download when ranking screened binders or explaining outputs.

Outputs

Rank from results/index.jsonl after download-results; use references/results.md for local file layout and metric meanings.