Protein MCP Server
by cyanheadsio.github.cyanheads/protein-mcp-serverv1.0.3
MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt.
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security
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cold start
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freshness
Active3d ago
Install Protein MCP server
Install in Claude Code
claude mcp add protein -- npx -y protein-mcp-server run start:stdioInstall in Cursor
{
"mcpServers": {
"protein": {
"command": "npx",
"args": [
"-y",
"protein-mcp-server",
"run",
"start:stdio"
]
}
}
}Add to ~/.cursor/mcp.json (global) or .cursor/mcp.json (project).
Install in Claude Desktop
{
"mcpServers": {
"protein": {
"command": "npx",
"args": [
"-y",
"protein-mcp-server",
"run",
"start:stdio"
]
}
}
}Settings → Developer → Edit Config (claude_desktop_config.json), then restart.
Install in VS Code
{
"servers": {
"protein": {
"type": "stdio",
"command": "npx",
"args": [
"-y",
"protein-mcp-server",
"run",
"start:stdio"
]
}
}
}Add to .vscode/mcp.json in your workspace.
Install in Windsurf
{
"mcpServers": {
"protein": {
"command": "npx",
"args": [
"-y",
"protein-mcp-server",
"run",
"start:stdio"
]
}
}
}Add to ~/.codeium/windsurf/mcp_config.json.
Configuration
| Variable | Required | Secret | Description |
|---|---|---|---|
| MCP_LOG_LEVEL | — | — | Sets the minimum log level for output (e.g., 'debug', 'info', 'warn'). |
| MCP_HTTP_HOST | — | — | The hostname for the HTTP server. |
| MCP_HTTP_PORT | — | — | The port to run the HTTP server on. |
| MCP_HTTP_ENDPOINT_PATH | — | — | The endpoint path for the MCP server. |
| MCP_AUTH_MODE | — | — | Authentication mode to use: 'none', 'jwt', or 'oauth'. |
Freshness
Active — last maintenance signal 3d ago. The newest of the signals below sets the band.
Last commit (default branch)
2026-10-07 · 3d ago · GitHub
Latest release
2026-10-07 · 3d ago · GitHub · v0.8.6
Package published
no data · npm/PyPI
Registry entry updated
2025-10-02 · 12mo ago · official registry · v1.0.3
FAQ
›How do I install the Protein MCP server in Claude Code?
Run: claude mcp add protein -- npx -y protein-mcp-server run start:stdio. For Cursor, VS Code, Claude Desktop and Windsurf, use the install tabs above.
›Does Protein require an API key?
No required environment variables are declared in its published metadata.
›Can I use Protein as a remote (hosted) MCP server?
Yes — it offers both a hosted endpoint and a local stdio package.
›Is Protein in the official MCP registry?
Yes, as io.github.cyanheads/protein-mcp-server.