Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add boltz-bio/boltz-api-skills --skill boltz-small-molecule-designgit clone --depth 1 https://github.com/boltz-bio/boltz-api-skillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/boltz-bio/boltz-api-skills/boltz-small-molecule-design)<a href="https://agentmods.dev/skills/boltz-bio/boltz-api-skills/boltz-small-molecule-design"><img src="https://agentmods.dev/badge/skills/boltz-bio/boltz-api-skills/boltz-small-molecule-design/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/boltz-bio/boltz-api-skills/boltz-small-molecule-design"><img src="https://agentmods.dev/badge/skills/boltz-bio/boltz-api-skills/boltz-small-molecule-design.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00045 | $0.01887 |
| Opus 5 | $0.00023 | $0.00944 |
| Sonnet 5 | $0.00009 | $0.00377 |
| Haiku 4.5 | $0.00005 | $0.00189 |
Grade A, and why
boltz-small-molecule-design scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 4d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 77 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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 wants de novo small-molecule binders (no existing library).
- Normalize the target: one or more protein sequences into
target.entities, plus optionalpocket_residues(0-based) and/orreference_ligands(known binders to help locate the pocket). - Pick
num_molecules— valid range 10 to 1,000,000 (server rejects outside it). If the user says fewer than 10, explain the floor and propose 10. - Only add
chemical_space(e.g."enamine_real") if the user explicitly wants generation restricted to synthesizable molecules within that library. - Supported optional features include
chemical_spaceandmolecule_filters; only add them on explicit request. Read references/api.md for exact shapes and filter options. - Author the payload YAML or JSON, run
estimate-cost, show the USD cost, wait for explicit confirmation. Cost is a flat $0.025 per molecule (size-independent); still quoteestimated_cost_usdfrom the response as the authoritative total. startto submit (synchronous). Capture the ID.- Launch
download-resultsthrough the runtime's long-running or non-blocking command facility; it polls, paginates, downloads per-hit structures, and exits when terminal. Use the mechanism the runtime documents; consultboltz-cli-setupif unsure. After launching the downloader, always report the job ID, run name, and output directory. If the runtime can schedule follow-up checks, schedule adownload-statuscheck and state the cadence; otherwise include thedownload-statuscommand. - Rank hits from
<output-root>/<run-name>/results/index.jsonlbybinding_confidencefor hit discovery oroptimization_scorefor lead optimization. Each generated molecule also carries a freeadmeblock (solubility,permeability,lipophilicity) — surface it for developability triage when the user cares about ADME, or when a top hit looks risky. Read references/results.md for output layout and metric details.
What ships with it
3 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 4d ago Changed · +10 lines · -29 tokens per session 1628673c1ee4
- 12d ago First seen · 67 lines · 74 tokens per session scan A fe4b6830df84
boltz-small-molecule-design is a skill published in the GitHub repository boltz-bio/boltz-api-skills (4 stars, last pushed 4d ago), licensed MIT. It adds 45 tokens to every session and 1,887 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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