Fastfold AI Skills

A collection of skills for AI agents. Skills are packaged instructions and scripts that extend agent capabilities.

Skills follow the Agent Skills format.

Install

npx skills add fastfold-ai/skills

Usage

Once installed, the agent uses a skill when the task matches its description and “Use when” triggers.

Example:

With .env set up (or FASTFOLD_API_KEY exported), run scripts without passing the key each time. Your agent can help you set this up—see Setting your FastFold API key below.

Just Ask:

Use Boltz-2 in Fastfold with affinity property to the ligand. Fold this protein: PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF and this ligand: CC1CN(CC(C1)NC(=O)C2=CC=CC=C2N)C(=O)NC(C)(C)C

Available Skills

Skills in this repo live in the skills/ folder.

fold

Submits and manages FastFold protein folding jobs via the Jobs API. Covers authentication, creating jobs, polling for completion, and fetching CIF/PDB URLs, metrics, and 3D viewer links.

Use when:

• Folding a protein sequence with FastFold (API or scripts)
• Mentioning FastFold API, fold job, CIF/PDB results, or viewer link
• Scripting: create job → wait for completion → download results / metrics / viewer URL

Features:

• Create Job (POST /v1/jobs) with sequences and params; optional constraints, library from ID
• Wait for completion with configurable polling and timeout
• Fetch results (JSON or summary), download CIF(s), get 3D viewer link
• Self-contained OpenAPI schema in references/jobs.yaml

Scripts:

• wait_for_completion.py – poll until COMPLETED/FAILED/STOPPED
• fetch_results.py – get job results summary (or --json for raw output)
• download_cif.py – download CIF file(s) for completed jobs
• get_viewer_link.py – print Mol* viewer URL: https://cloud.fastfold.ai/mol/new?from=jobs&job_id=<id>

Requires: FASTFOLD_API_KEY from .env or environment. Agent will ask the user to set it locally before continuing if missing.

slack_report

Share markdown reports to Slack and save a copy to Fastfold library.

Use when:

• Sharing an agent/session report to a Slack channel
• Posting markdown summaries to team updates
• Saving the same report in library and Slack in one step

Features:

• Sends report via POST /v1/slack/messages/agent-cli-report
• Uses configured agent_cli_report channel in Slack integrations
• Returns friendly guidance when Slack is not configured
• Includes library open link when library_item_id is returned

Scripts:

• send_agent_cli_report.py – send markdown report to Slack report channel and save to library

Requires: FASTFOLD_API_KEY from environment or .env.

Setting your FastFold API key

Scripts automatically read FASTFOLD_API_KEY from a .env file in the project (current directory or any parent), so you don't need to export it in the shell.

Option A — Use a .env file (recommended)

1. Copy the template: cp skills/fold/references/.env.example .env
2. Open .env and paste your API key after the =:
   FASTFOLD_API_KEY=sk-your-actual-key-here
3. Save. Scripts will load the key when you run them from this repo or any subdirectory.

Get a key at FastFold API Keys. Do not commit .env (it's in .gitignore). Do not paste API keys in chat; keep secrets in local .env only.

Option B — Export in the shell: export FASTFOLD_API_KEY="sk-..."
Environment variables take precedence over .env.

License

MIT