Fastfold AI Docs - FastFold Agent CLI

Autonomous AI research agent for drug discovery — ask questions in natural language and get data-backed answers.

FastFold Agent CLI — Autonomous Drug Discovery Agent

The FastFold Agent CLI (fastfold) is an autonomous research agent for drug discovery. Ask questions in natural language — it plans the analysis, selects the right tools, executes them, validates results, and returns data-backed conclusions. Integrates with FastFold AI Cloud for GPU compute, protein folding, and workflow orchestration.

PyPI: fastfold-agent-cli
GitHub: fastfold-ai/fastfold-agent-cli

Installation

Requires Python 3.10 or later.

uv tool install "fastfold-agent-cli[all]" --python 3.10

If you see Python>=3.10 not satisfied, your system Python is too old. Run uv python install 3.10 first, then retry the install command above.

Via fastfold-cli (auto-install)

If you already have the FastFold CLI installed, the agent is launched — and installed automatically on first run — with:

fastfold-cli agent "your question here"

Authentication

fastfold setup

Quick start

# Start interactive session
fastfold

# Single query
fastfold "What are the top degradation targets for this compound?"

# Validate your setup
fastfold doctor

Example queries

Target prioritization

fastfold "I have a CRBN molecular glue. Proteomics shows it degrades IKZF1, GSPT1,
          and CK1α. Which target should I prioritize?"

Protein folding

fastfold "Fold this sequence with boltz-2 and find the binding pockets: MALWMRLLPLL..."

Combination strategy

fastfold "My lead compound is immune-cold. What combination strategy should I use?"

Interactive mode commands

Inside fastfold interactive mode:

Command	Description
`/help`	Command reference and examples
`/tools`	List all tools with status
`/agents N <query>`	Run N parallel research agents
`/sessions`, `/resume`	Session lifecycle
`/copy`, `/export`	Save or share outputs
`/usage`	Token and cost tracking

Tool categories

Category	Examples
Target	Neosubstrate scoring, degron prediction, co-essentiality networks
Chemistry	SAR analysis, fingerprint similarity, scaffold clustering
Expression	L1000 signatures, pathway enrichment, TF activity, immune scoring
Viability	Dose-response modeling, PRISM screening, therapeutic windows
Structure	AlphaFold fetch, docking, binding sites, MD simulation
Folding	FastFold AI Cloud: boltz-2, monomer, multimer, simplefold_*
Literature	PubMed, OpenAlex, ChEMBL search
DNA	ORF finding, codon optimization, primer design

fastfold tool list    # see all 190+ tools
fastfold skill list   # see loaded skills

Data management

fastfold data pull depmap    # DepMap CRISPR, mutations, expression
fastfold data pull prism     # PRISM cell viability
fastfold data pull msigdb    # Gene sets

# Or point to existing data
fastfold config set data.depmap /path/to/depmap/

Reports

fastfold report list      # list saved reports
fastfold report publish   # convert latest .md to .html
fastfold report show      # open in browser

Troubleshooting

Symptom	Fix
`fastfold` fails at startup	`fastfold doctor`
No API key error	`fastfold setup` or `export ANTHROPIC_API_KEY=...`
Data not found	`fastfold data pull <dataset>`
Missing dependency	`pip install "fastfold-agent-cli[all]"`
Session lost	`fastfold --continue`

Next steps

Submit folding jobs directly from scripts → FastFold CLI
Python SDK for programmatic workflows → Python SDK

FastFold Agent CLI

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