How do I install Protein?

Protein is a local plugin. Install it using npm package: protein-mcp-server and add the generated configuration snippet to your AI app's MCP config file. Then restart your AI app.

What credentials does Protein need?

Protein requires the following credentials or environment variables: MCP_LOG_LEVEL, MCP_HTTP_HOST, MCP_HTTP_PORT, MCP_HTTP_ENDPOINT_PATH, MCP_AUTH_MODE. You can find setup instructions on the server detail page.

What AI apps work with Protein?

Protein uses the Model Context Protocol (MCP) and works with any MCP-compatible AI app, including Claude, ChatGPT / Codex, Gemini, Copilot, Cursor, and more.

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Protein MCP Server

by Cyanheads

Developer ToolsModerate5.7MCP RegistryLocal

Free

Server data from the Official MCP Registry

MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt.

About

MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt.

Security Report

5.7

Moderate5.7Moderate Risk

Valid MCP server (1 strong, 1 medium validity signals). 5 known CVEs in dependencies (0 critical, 4 high severity) Package registry verified. Imported from the Official MCP Registry. Trust signals: 6 highly-trusted packages.

4 files analyzed · 6 issues found

Security scores are indicators to help you make informed decisions, not guarantees. Always review permissions before connecting any MCP server.

What You'll Need

Set these up before or after installing:

Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').Optional

Environment variable: MCP_LOG_LEVEL

The hostname for the HTTP server.Optional

Environment variable: MCP_HTTP_HOST

The port to run the HTTP server on.Optional

Environment variable: MCP_HTTP_PORT

The endpoint path for the MCP server.Optional

Environment variable: MCP_HTTP_ENDPOINT_PATH

Authentication mode to use: 'none', 'jwt', or 'oauth'.Optional

Environment variable: MCP_AUTH_MODE

How to Install

Add this to your MCP configuration file:

{
  "mcpServers": {
    "io-github-cyanheads-protein-mcp-server": {
      "env": {
        "MCP_AUTH_MODE": "your-mcp-auth-mode-here",
        "MCP_HTTP_HOST": "your-mcp-http-host-here",
        "MCP_HTTP_PORT": "your-mcp-http-port-here",
        "MCP_LOG_LEVEL": "your-mcp-log-level-here",
        "MCP_HTTP_ENDPOINT_PATH": "your-mcp-http-endpoint-path-here"
      },
      "args": [
        "-y",
        "protein-mcp-server"
      ],
      "command": "npx"
    }
  }
}

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Security Report

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Moderate5.7Moderate Risk

4 files analyzed · 6 issues found

Security scores are indicators to help you make informed decisions, not guarantees. Always review permissions before connecting any MCP server.

What You'll Need

Set these up before or after installing:

Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').Optional

Environment variable: MCP_LOG_LEVEL

The hostname for the HTTP server.Optional

Environment variable: MCP_HTTP_HOST

The port to run the HTTP server on.Optional

Environment variable: MCP_HTTP_PORT

The endpoint path for the MCP server.Optional

Environment variable: MCP_HTTP_ENDPOINT_PATH

Authentication mode to use: 'none', 'jwt', or 'oauth'.Optional

Environment variable: MCP_AUTH_MODE

{ "mcpServers": { "io-github-cyanheads-protein-mcp-server": { "env": { "MCP_AUTH_MODE": "your-mcp-auth-mode-here", "MCP_HTTP_HOST": "your-mcp-http-host-here", "MCP_HTTP_PORT": "your-mcp-http-port-here", "MCP_LOG_LEVEL": "your-mcp-log-level-here", "MCP_HTTP_ENDPOINT_PATH": "your-mcp-http-endpoint-path-here" }, "args": [ "-y", "protein-mcp-server" ], "command": "npx" } } }

Protein MCP Server

About

Security Report

Findings (6)Action required

What You'll Need

How to Install

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