Used for installation and building the MCP server.
Supports downloading structure coordinates in XML format alongside other formats like PDB, mmCIF, and mmTF.
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
Usage
With Claude Desktop
Add to your claude_desktop_config.json
:
Example Queries
Search for insulin structures:
Use the search_structures tool to find insulin protein structuresGet information about a specific structure:
Get detailed information about PDB structure 1ABC using get_structure_infoDownload structure coordinates:
Download the PDB file for structure 1ABC using download_structureFind structures for a UniProt protein:
Find PDB structures for UniProt accession P01308 using search_by_uniprotCheck structure quality:
Get validation metrics for PDB structure 1ABC using get_structure_qualityAccess 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
Attribution
This project is developed by Augmented Nature š Website: augmentednature.ai
Citation
If you use this project in your research or publications, please cite it as follows:
remote-capable server
The server can be hosted and run remotely because it primarily relies on remote services or has no dependency on the local environment.
PDB MCP Server
- Features
- Installation
- Usage
- API Integration
- Structure Data Formats
- Quality Metrics
- Complementary Servers
- Error Handling
- Development
- Attribution
- Citation
Related Resources
Related MCP Servers
- MIT License
- Apache 2.0