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MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt.
44FairInstall
~/Library/Application Support/Claude/claude_desktop_config.json
{
"mcpServers": {
"cyanheads-protein-mcp-server": {
"command": "bun",
"args": [
"-y",
"protein-mcp-server@1.0.3"
],
"env": {
"MCP_LOG_LEVEL": "info"
}
}
}
}
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Environment
| Name | Required | Notes |
|---|
| MCP_LOG_LEVEL | No | Sets the minimum log level for output (e.g., 'debug', 'info', 'warn'). |
| MCP_HTTP_HOST | No | The hostname for the HTTP server. |
| MCP_HTTP_PORT | No | The port to run the HTTP server on. |
| MCP_HTTP_ENDPOINT_PATH | No | The endpoint path for the MCP server. |
| MCP_AUTH_MODE | No | Authentication mode to use: 'none', 'jwt', or 'oauth'. |
| MCP_LOG_LEVEL | No | Sets the minimum log level for output (e.g., 'debug', 'info', 'warn'). |
Tools show up when the registry metadata or the repository README lists them. GitHub enrichment fills this in when a token is configured.
About
Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.
FAQ
- What is protein-mcp-server?
- MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt.
- How do I install protein-mcp-server?
- Pick a client above and copy the generated config. Cursor and VS Code also have a deep link when the server can run locally or remotely.
- Is protein-mcp-server official?
- No. Registry-listed is not the same as vendor-official. Read the methodology for the difference.
- How is the trust score calculated?
- This listing scores 44 (Fair). The formula is published on the methodology page.
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