ProteinIQ MCP MCP server

An official MCP server provided by ProteinIQ that allows AI agents to interact with bioinformatics tools. It enables agents to select tools, quote costs, submit jobs for protein folding, docking, and design, and read results directly within the agent's workspace using a workspace API key.

Endpoint and access

OAuth sign-in: the first time you connect, your client opens the vendor's own authorization prompt in a browser.

OAuth sign-inEndpoint checked 2026-10-05Operated by ProteinIQ

MCP endpoint (Streamable HTTP)

https://proteiniq.io/mcp

Vendor documentation

What you can do with it

Predict protein structure using ESMFold and analyze confidence regions
Perform batch molecular docking of SMILES against a receptor with budget limits
Search tool catalog to recommend methods for antibody-antigen binding prediction
Create and validate workflows combining Boltz-2 and PoseBusters

Connect from your client

Each snippet registers the same endpoint; pick the client you use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Claude Code

Run this once in a terminal. It registers a Streamable HTTP server. Use --scope project to write .mcp.json for the repo.

Claude Code configuration

claude mcp add --transport http proteiniq-mcp https://proteiniq.io/mcp

Codex

Run this once. Codex stores MCP servers in ~/.codex/config.toml (or .codex/config.toml in a trusted project).

Codex configuration

codex mcp add proteiniq-mcp --url https://proteiniq.io/mcp

Cursor

Merge this server into .cursor/mcp.json in your project, then enable proteiniq-mcp in your MCP settings.

Cursor configuration

{
  "mcpServers": {
    "proteiniq-mcp": {
      "url": "https://proteiniq.io/mcp"
    }
  }
}

Cline

Merge this into cline_mcp_settings.json (Cline → MCP Servers → Configure). The type must be streamableHttp for a remote HTTP server.

Cline configuration

{
  "mcpServers": {
    "proteiniq-mcp": {
      "type": "streamableHttp",
      "url": "https://proteiniq.io/mcp",
      "disabled": false
    }
  }
}

VS Code

Merge this server into .vscode/mcp.json. Use MCP: List Servers to start proteiniq-mcp and inspect its tools.

VS Code configuration

{
  "servers": {
    "proteiniq-mcp": {
      "type": "http",
      "url": "https://proteiniq.io/mcp"
    }
  }
}

Gemini CLI

Run this once. It writes .gemini/settings.json in the current project; pass --scope user for ~/.gemini/settings.json.

Gemini CLI configuration

gemini mcp add --transport http proteiniq-mcp https://proteiniq.io/mcp

Claude Desktop

Merge this into claude_desktop_config.json (macOS: ~/Library/Application Support/Claude/, Windows: %APPDATA%\Claude\), then restart Claude Desktop.

Claude Desktop configuration

{
  "mcpServers": {
    "proteiniq-mcp": {
      "url": "https://proteiniq.io/mcp"
    }
  }
}

Windsurf

Merge this into ~/.codeium/windsurf/mcp_config.json, then refresh MCP in Cascade. Windsurf remote servers use serverUrl, not url.

Windsurf configuration

{
  "mcpServers": {
    "proteiniq-mcp": {
      "serverUrl": "https://proteiniq.io/mcp"
    }
  }
}

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