Refua

Fold and score biomolecular complexes and optionally profile ADMET to prioritize molecules in drug discovery pipelines via the refua-mcp server.

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)

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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

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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

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Running the MCP server

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

bash

python3 -m refua_mcp.server