Refua

Skill: Refua

Summary

Refua is used in drug discovery to computationally fold and score biomolecular complexes (e.g., protein–ligand/protein–protein) and optionally profile ADMET, helping prioritize which molecules to synthesize and test first in a drug discovery pipeline.

This skill runs and connects to the refua-mcp MCP server, which exposes Refua’s “unified Complex API” as MCP tools for:

• Boltz2 complex folding (+ optional affinity evaluation)
• BoltzGen design workflows
• Optional ADMET profiling (when installed)

Clawdbot supports MCP natively, so the only requirement is running this MCP server and calling its tools. (github.com)

When to use

Use this skill when you need to:

• Fold a protein–ligand, protein–protein, or (fold-only) DNA/RNA complex
• Estimate binding affinity for a specified binder within a complex spec
• Run ADMET predictions for one or more SMILES ligands (if enabled)
• Execute GPU/CPU-heavy Refua workflows via MCP tool calls

Do NOT use this skill when:

• The task is a simple deterministic calculation (prefer a non-ML tool)
• The user expects you to invent sequences/SMILES (request inputs instead)
• The user requests unsafe wet-lab or clinical guidance

Installation & assets (operator steps)

1) Install Refua + refua-mcp

Install Refua (CPU or CUDA), then install the MCP server package: (github.com)

• GPU support:
  • pip install refua[cuda]
• CPU-only:
  • pip install refua
• MCP server:
  • pip install refua-mcp

2) Optional: enable ADMET

ADMET tool support is optional and requires an extra: (github.com)

• pip install refua[admet]

3) Download model/assets

Boltz2 and BoltzGen require model/molecule assets. Refua can download them automatically: (github.com)

• python -c "from refua import download_assets; download_assets()"

Default asset locations + overrides: (github.com)

• Boltz2 uses ~/.boltz by default
  • Override via tool option boltz.cache_dir if needed
• BoltzGen uses a bundled HF artifact by default
  • Override via tool option boltzgen.mol_dir if needed

Running the MCP server

Start the server using the module entrypoint: (github.com)

python3 -m refua_mcp.server