Fastfold AI Docs - FastFold CLI

The FastFold CLI (fastfold-cli) is ideal for quick experiments, shell scripts, and CI pipelines. It ships as part of the fastfold-ai Python package.

Installation

pip install fastfold-ai

Authentication

export FASTFOLD_API_KEY="sk-...your-api-key"

You can also pass the key explicitly via --api-key.

Submit a folding job

fastfold-cli fold --sequence "LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES" --model boltz-2

On success, the CLI prints the created job ID to stdout.

Common flags

fastfold-cli fold \
  --sequence "..." \
  --model boltz-2 \
  --name "My Job" \
  --api-key "sk-..." \
  --base-url "https://api.fastfold.ai"

CI-friendly pattern

export FASTFOLD_API_KEY="$FASTFOLD_API_KEY"
fastfold-cli fold --sequence "$SEQ" --model boltz-2 --name "ci-$GITHUB_RUN_ID"

Launch the AI research agent

fastfold-cli includes an agent subcommand that installs and launches the FastFold Agent CLI automatically:

fastfold-cli agent "What are the top EGFR inhibitors for lung cancer?"

If fastfold-agent-cli is not yet installed, it will be pulled from PyPI on first run.

Next steps

Full agent workflows and interactive mode → FastFold Agent CLI
Artifact URLs, metrics, and wait-for-completion → Python SDK examples

FastFold CLI