{
  "markdown": "# Boltz Skills\n\nRun Boltz biomolecular workflows — structure prediction, binding, molecular and\nprotein screening, and de novo design — directly from your AI coding agent.\nThe skills shell out to the [`boltz-api`](https://install.boltz.bio) CLI to\ncreate inputs, estimate cost, submit jobs, and download results.\n\n📖 **Full guide:** [Agent integrations for the Boltz API](https://api.boltz.bio/docs/guides/agent-integrations/)\n\n## Supported agents\n\nFor Codex and Claude Code, use the official marketplace plugins. Gemini CLI\nhas a native extension, and Claude Desktop uses the MCPB server.\n[Vercel Skills](https://github.com/vercel-labs/skills) provides an additional\nway to install the shared skills in Antigravity and other supported agents,\nor in environments where you prefer a direct skill installation.\n\n## Skills\n\n| Skill | What it does |\n|---|---|\n| `boltz-cli-setup` | Install, update, verify, and authenticate the `boltz-api` CLI. |\n| `boltz-structure-and-binding` | Predict the 3D structure of a defined complex; optionally score binding. |\n| `boltz-small-molecule-screen` | Rank a SMILES library against a target. |\n| `boltz-small-molecule-design` | Generate novel small-molecule binders. |\n| `boltz-small-molecule-adme` | Estimate Tier-1 ADME (solubility, permeability, logD) from bare SMILES. |\n| `boltz-protein-screen` | Rank proteins / peptides / antibodies against a target. |\n| `boltz-protein-design` | Generate novel peptide / antibody / nanobody / custom-protein binders. |\n| `boltz-check-status` | List and inspect jobs; recover results after an interrupted session. |\n\n## Prerequisites\n\nAll surfaces need the `boltz-api` CLI on your `PATH`.\n\n**macOS and Linux:**\n\n```sh\ncurl -fsSL https://install.boltz.bio/boltz-api/install.sh | sh\n```\n\n**Windows PowerShell:**\n\n```powershell\nirm https://install.boltz.bio/boltz-api/install.ps1 | iex\n```\n\nVerify it:\n\n```sh\nboltz-api --version\n```\n\nThen authenticate, using either device-code login or an API key:\n\n```sh\nboltz-api auth login --device-code\n# or\nexport BOLTZ_API_KEY=\"your-api-key\"\n```\n\nResults download to a `boltz-experiments/` directory in your working directory\n(created automatically). Point any command at a different location with\n`--root-dir`.\n\n## Install\n\n### Codex and Claude Code (recommended: official plugins)\n\nFor Codex, open the plugin directory, search for **Boltz**, and install the\nofficial plugin. In Codex CLI, enter `/plugins` to open the plugin browser.\nStart a new session after installing. See the\n[Codex installation guide](surfaces/codex-cli/README.md) for details.\n\nFor Claude Code, follow the\n[marketplace installation guide](surfaces/claude-code-cli/README.md).\n\nBoth plugins use `boltz-api`; complete the prerequisites above or ask for\n`boltz-cli-setup`.\n\n### Other agents and direct skill installation\n\nUse [Vercel Skills](https://github.com/vercel-labs/skills) with Node.js 22.20 or\nnewer. Select your agents and skills interactively:\n\n```sh\nnpx skills add boltz-bio/boltz-api-skills\n```\n\nFor example, install all eight skills for Gemini CLI in the current project:\n\n```sh\nnpx skills add boltz-bio/boltz-api-skills --skill '*' --agent gemini-cli\n```\n\nAdd `--global` to make the skills available across projects. Use `--list` to\npreview the available skills without installing. Use `--copy` if your host\ncannot use symlinks. Skills installation does not install or authenticate the\n`boltz-api` CLI; complete the prerequisites above or ask for `boltz-cli-setup`.\n\nUse one installation method per agent and scope to avoid loading the same\nskills twice. Direct Skills installation is optional for Codex and Claude\nCode; existing marketplace users can keep their plugin installation.\n\nTo install selected skills, pass their names to `--skill`. Include\n`boltz-cli-setup` if you need help installing or authenticating the CLI:\n\n```sh\nnpx skills add boltz-bio/boltz-api-skills --skill boltz-cli-setup boltz-protein-design --agent gemini-cli\n```\n\nFor direct Skills installations, keep the generated `skills-lock.json` with\nyour project. Updates are explicit; review the resulting file changes:\n\n```sh\nnpx skills update boltz-cli-setup boltz-protein-design --project\n```\n\nUse your agent's plugin manager to update marketplace installations.\n\n### Gemini extension\n\nGemini CLI users can also use the\n[native extension](surfaces/gemini-cli/README.md).\n\n### Claude Desktop\n\nDownload the latest `boltz-mcpb-<version>.mcpb` from\n[Releases](https://github.com/boltz-bio/boltz-api-skills/releases) and install it\nvia **Settings → Extensions → Advanced settings → Install Extension**.\n\nRestart your agent after installing.\n\n## Usage\n\nOnce installed and authenticated, just describe what you want in natural\nlanguage — the agent picks the right skill, builds the payload, shows you a cost\nestimate before submitting, and downloads results when the job finishes. For\nexample:\n\n> Predict the structure of this protein–ligand complex and score the binding affinity.\n\n> Screen these 200 SMILES against my target and rank them.\n\nSee the [full guide](https://api.boltz.bio/docs/guides/agent-integrations/) for\ndetailed workflows and examples.\n\n## Repository layout\n\n- `skills/<name>/` — canonical public skills with instructions, references,\n  optional helper scripts, and agent metadata.\n- `surfaces/` — marketplace and extension wrappers and the Claude Desktop MCPB runtime.\n  CLI wrappers link to `skills/`; the partner bundle retains its distinct\n  host-managed authentication and spending policy.\n- `plugins/` — generated, self-contained marketplace and MCPB copies.\n- `tests/` — distribution checks and protein-design helper tests.\n\n## Local development\n\nEdit `skills/` for shared workflow changes. Then regenerate and verify the\nmarketplace and MCPB packages:\n\n```sh\nnpm ci\nscripts/generate-surfaces.sh\nnpm test\nscripts/verify-generated.sh\n```\n\nThe install tests use the pinned Skills CLI to install into temporary projects\nfor Claude Code, Codex, and Gemini CLI. They do not install into your agents or\nsubmit Boltz jobs.\n\nSee [CONTRIBUTING.md](CONTRIBUTING.md) for runtime tests and release workflows.\n\n## License\n\nMIT — see [`LICENSE`](LICENSE).\n",
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