Refua MCP

An MCP server that exposes strict, typed Refua tools for Boltz-2 folding, affinity prediction, and BoltzGen design workflows, making drug discovery accessible to any AI assistant.

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8 Typed Tools
MCP Protocol
3 Transport Modes
Async Job Support

What Is Refua MCP?

Refua MCP is a Model Context Protocol server that bridges AI assistants and the Refua drug discovery toolkit. It exposes typed, schema-validated tools that any MCP-compatible client can call to perform protein folding, affinity prediction, antibody design, ADMET profiling, and clinical simulation.

The server follows the MCP spec revision 2025-11-25 and supports stdio, SSE, and streamable-HTTP transports with configurable security controls.

Available Tools

  • refua_fold – Fold/design with entities and constraints
  • refua_affinity – Affinity-only predictions
  • refua_antibody_design – Antibody CDR design
  • refua_validate_spec – Pre-flight validation
  • refua_protein_properties – Sequence-based analysis
  • refua_admet_profile – ADMET predictions
  • refua_clinical_simulator – Trial simulation
  • refua_job – Background job management

Works With Your AI Tools

🤖

Claude Code

Add Refua MCP to your Claude Code configuration and let Claude perform protein folding, design antibodies, and predict ADMET properties.

💻

Codex

Register with codex mcp add and use Refua tools from the Codex CLI for AI-powered drug discovery workflows.

🔌

Any MCP Client

Refua MCP follows the open MCP protocol spec, so any compatible client can connect via stdio, SSE, or HTTP transports.

Resources & Recipes

The server exposes rich metadata resources and recipe templates to help AI assistants discover capabilities and construct valid tool calls.

📖

Capabilities Resource

Runtime feature flags, protocol revision, transport config, and security summary available at refua://capabilities.

🧪

Recipe Templates

Canonical recipes for fold, affinity, antibody design, protein properties, and clinical simulation at refua://recipes/{name}.

🧬

Protein Property Catalog

Browse available property groups and individual property metadata through refua://protein-properties/ resources.

Security & Transport

Refua MCP supports three transport modes: stdio (default), SSE, and streamable-HTTP. HTTP transports include DNS rebinding protection, allowed hosts/origins configuration, and static bearer token authentication.

All major tools enforce strict JSON schemas with discriminated entity unions, and exploratory names are blocked by default to prevent costly preflight runs.

Security Controls

  • DNS rebinding protection
  • Allowed hosts and origins configuration
  • Static bearer token authentication for HTTP
  • Task timeout and queue timeout controls
  • Exploratory run blocking by default

Get Started

Installation

pip install refua[cuda] refua-mcp

Optional ADMET and clinical extras:

pip install "refua[admet]" "refua-mcp[clinical]"

Run the Server

python -m refua_mcp.server

Or with HTTP transport:

REFUA_MCP_TRANSPORT=streamable-http python -m refua_mcp.server

Give Your AI Drug Discovery Tools

Refua MCP lets any AI assistant access the full power of the Refua toolkit through a standards-based protocol with strict type safety and security controls.

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