Skills

Fastfold skills are packaged instructions and scripts that help AI agents run common workflows end-to-end.

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

Install

npx skills add fastfold-ai/skills

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

Available skills

fold

Fastfold Jobs API automation for protein folding.

Use it when you need:

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

References:

• Skill: skills/fold/SKILL.md
• Auth/API: skills/fold/references/auth_and_api.md
• Schema summary: skills/fold/references/schema_summary.md
• OpenAPI reference: skills/fold/references/jobs.yaml

md-openmm-calvados

CALVADOS + OpenMM workflow automation via Workflows API (calvados_openmm_v1).

Use it when you need:

• fold -> OpenMM linked simulation flows
• manual PDB + PAE submission for MD simulation
• MD metrics, artifacts, and result polling

References:

• Skill: skills/md-openmm-calvados/SKILL.md
• Auth/API: skills/md-openmm-calvados/references/auth_and_api.md
• Schema summary: skills/md-openmm-calvados/references/schema_summary.md
• Method details: skills/md-openmm-calvados/references/calvados_method.md

md-openmmdl

OpenMMDL protein-ligand molecular dynamics workflow automation via Workflows API (openmmdl_v1).

Use it when you need:

• topology + ligand-driven MD workflow submission
• draft script preparation + execution for OpenMMDL
• analysis outputs, trajectory artifacts, and frame extraction

References:

• Skill: skills/md-openmmdl/SKILL.md
• Auth/API: skills/md-openmmdl/references/auth_and_api.md
• Schema summary: skills/md-openmmdl/references/schema_summary.md

protein_design_boltzgen

BoltzGen protein design workflow automation (draft -> graph upsert -> review -> execute -> ranked results).

Use it when you need:

• single-spec or multi-spec BoltzGen design flows
• example-first workflow setup from bundled local preset files
• candidate metrics interpretation and per-candidate Mol* result links
• API-only workflow orchestration that mirrors Composer behavior

References:

• Skill: skills/protein_design_boltzgen/SKILL.md
• Workflow helper script: skills/protein_design_boltzgen/scripts/workflow_api.py
• YAML keys: skills/protein_design_boltzgen/references/yaml_keys.md
• Preset examples: skills/protein_design_boltzgen/references/examples/README.md
• Metrics guide: skills/protein_design_boltzgen/references/metrics_guide.md

slack_report

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

Use it when you need:

• share a markdown report to Slack
• keep a saved copy in Fastfold library
• give teammates a quick link to open the saved report

References:

• Skill: skills/slack_report/SKILL.md
• API reference: skills/slack_report/references/api.md

Example prompts

After installing, 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

Run an OpenMM simulation from my completed fold job and return metrics, plots, and the dashboard link.

Run an OpenMMDL simulation with topology + ligand inputs and return analysis outputs with links.

Help me run a quick BoltzGen smoke test for a simple peptide binder against 5CQG, and show me the draft before running.

Show me BoltzGen protein design examples and run vanilla_target_binding_site with one target and one budget in the background. Keep the workflow_id for follow-up results.

Share the current report to Slack and save a copy in my Fastfold library.

API key setup

Skills and 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.

Slack setup for slack_report

Before using /export-share, connect Slack and set a channel in Fastfold Cloud:

• cloud.fastfold.ai/integrations/slack

Set or confirm the channel for the agent_cli_report mode.

Security note

Keep API keys local and never commit .env files.