AlphaFold

The AlphaFold MCP Server provides programmatic access to the AlphaFold Protein Structure Database through a rich set of tools for retrieval, analysis, batch processing, and visualization preparation. You can discover, fetch, and compare predicted structures by UniProt ID, search for proteins by name or organism, evaluate per-residue confidence scores, and generate export-ready formats for PyMOL or ChimeraX. The server exposes a collection of MCP tools such as get_structure, download_structure, check_availability, search_structures, get_confidence_scores, batch_structure_info, batch_download, compare_structures, find_similar_structures, and export_for_pymol/export_for_chimerax, enabling streamlined workflows from discovery to visualization-ready data.

Prerequisites:\n- Node.js (and npm) installed on your system.\n- Access to the repository hosting the AlphaFold MCP Server.\n\nInstallation steps:\n1) Clone or create the server directory:\n git clone <repository-url> alphafold-server\n cd alphafold-server\n\n2) Install dependencies:\n npm install\n\n3) Build the server (if a build step is required by the project):\n npm run build\n\n4) Run the server (as a local MCP server):\n npm start\n // Or start directly if you run the built file:\n node build/index.js\n\nNote: The MCP configuration for integrating this server into an MCP platform should reference the server entry as shown in the mcp_config section.

Tips and considerations:\n- Ensure Node.js runtime matches the server’s compatibility (check package.json for engines).\n- The MCP config uses the server name alphafold-server; ensure consistency across your platform.\n- When retrieving large batches, leverage batch_* tools to minimize round-trips and optimize throughput.\n- For visualization exports, confirm that downstream tools (PyMOL/ChimeraX) are prepared to consume the exported formats.\n- If the server cannot reach AlphaFold data sources, verify network access and any API endpoints or data mirrors used by the implementation.\n- Environment variables you may need to configure (placeholders):\n - ALPHAFOLD_API_BASE_URL: Base URL for AlphaFold API (if applicable).\n - LOG_LEVEL: Information, debug, or warning level for verbose logs.\n - DATA_CACHE_DIR: Path to cache downloaded structures to improve performance.