PDB MCP Server

 # PDB MCP Server A Model Context Protocol (MCP) server that provides access to the Protein Data Bank (PDB) - the worldwide repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies. ## Features ### Tools - **search_structures**: Search PDB database for protein structures by keyword, protein name, or PDB ID - **get_structure_info**: Get detailed information for a specific PDB structure - **download_structure**: Download structure coordinates in various formats (PDB, mmCIF, mmTF, XML) - **search_by_uniprot**: Find PDB structures associated with a UniProt accession - **get_structure_quality**: Get structure quality metrics and validation data ### Resources - **pdb://structure/{pdb_id}**: Complete structure information for a PDB ID - **pdb://coordinates/{pdb_id}**: Structure coordinates in PDB format - **pdb://mmcif/{pdb_id}**: Structure data in mmCIF format - **pdb://validation/{pdb_id}**: Structure validation data and quality metrics - **pdb://ligands/{pdb_id}**: Ligand and binding site information - **pdb://search/{query}**: Search results for structures matching the query ## Installation ```bash npm install npm run build ``` ## Usage ### With Claude Desktop Add to your `claude_desktop_config.json`: ```json { "mcpServers": { "pdb-server": { "command": "node", "args": ["/path/to/pdb-server/build/index.js"] } } } ``` ### Example Queries 1. **Search for insulin structures**: ``` Use the search_structures tool to find insulin protein structures ``` 2. **Get information about a specific structure**: ``` Get detailed information about PDB structure 1ABC using get_structure_info ``` 3. **Download structure coordinates**: ``` Download the PDB file for structure 1ABC using download_structure ``` 4. **Find structures for a UniProt protein**: ``` Find PDB structures for UniProt accession P01308 using search_by_uniprot ``` 5. **Check structure quality**: ``` Get validation metrics for PDB structure 1ABC using get_structure_quality ``` 6. **Access resources directly**: ``` Show me the resource pdb://structure/1abc ``` ## API Integration This server integrates with: - **RCSB PDB REST API** (https://data.rcsb.org/): For structure metadata and information - **RCSB PDB Search API** (https://search.rcsb.org/): For advanced search capabilities - **RCSB PDB File Download** (https://files.rcsb.org/): For structure file downloads ## Structure Data Formats - **PDB**: Original Protein Data Bank format - **mmCIF**: Macromolecular Crystallographic Information File (newer standard) - **mmTF**: Macromolecular Transmission Format (binary, compressed) - **XML**: Extensible Markup Language format ## Quality Metrics The server provides various structure quality indicators: - Resolution (for X-ray crystallography) - R-work and R-free values - Ramachandran plot statistics - Clash scores - Rotamer outliers - Model validation scores ## Complementary Servers This PDB server works well with: - **UniProt MCP Server**: For protein sequence and functional information - **AlphaFold MCP Server**: For predicted protein structures Together, these provide comprehensive access to protein structure and function data. ## Error Handling The server includes robust error handling for: - Invalid PDB IDs - Network connectivity issues - API rate limiting - Missing structure files - Malformed requests ## Development ```bash # Install dependencies npm install # Build the server npm run build # Run in development mode npm run dev ``` ## Attribution This project is developed by **Augmented Nature** 🌐 Website: [augmentednature.ai](https://augmentednature.ai) ## Citation If you use this project in your research or publications, please cite it as follows: ```bibtex @misc{pdbmcp2025, author = {Moudather Chelbi}, title = {Protein Data Bank (PDB) MCP Server}, year = {2025}, howpublished = {https://github.com/Augmented-Nature/PDB-MCP-Server}, note = {Accessed: 2025-06-29}