Skills for Agents

Fastfold Skills are packaged instructions and scripts that help AI agents run fold workflows end-to-end with the Fastfold Jobs API.

These skills can be used across many agent tools (for example Claude Code, Cursor, Codex, and others). See skills.sh for the full list of supported agents.

Install

npx skills add fastfold-ai/skills

Repository: github.com/fastfold-ai/skills
Listing: skills.sh/fastfold-ai/skills

Example

After installing, you can ask your agent directly:

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

Usage

Once installed, your agent can invoke the skill when requests match folding tasks.

Typical flow:

• create fold job
• wait for completion
• fetch results and metrics
• get artifact URLs (CIF/PDB)
• generate viewer links

Available skill: fold

The fold skill is designed for Fastfold Jobs API automation.

Use it when you need:

• protein sequence folding with Fastfold
• API or script-based job orchestration
• automated create -> wait -> fetch pipelines

Features

• Create Job (POST /v1/jobs) with sequences, params, constraints, and optional library from ID
• Wait for completion with configurable polling and timeout
• Fetch results summary (or raw JSON)
• Download CIF outputs
• Generate 3D viewer links

Included scripts

• wait_for_completion.py
• fetch_results.py
• download_cif.py
• get_viewer_link.py

API key setup

Skills/scripts require FASTFOLD_API_KEY.

Option A: .env (recommended)

Your agent can help you create these files and follow the setup.

cp skills/fold/references/.env.example .env

Then edit .env:

FASTFOLD_API_KEY=sk-your-actual-key-here

Option B: shell environment

export FASTFOLD_API_KEY="sk-..."

Environment variables take precedence over .env.

Security note

Keep API keys local and never commit .env files.