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Project description
Protein Data Bank MCP Server
Micro-service for accessing the Protein Data Bank (PDB) API through the MCP protocol. This service provides structured access to protein structures, chemical components, and related annotations from the PDB database.
Features
- Access to PDB core API endpoints
- Structured data retrieval for proteins, assemblies, and chemical components
- Support for annotation data from DrugBank, UniProt, and PubMed
- Built on FastMCP framework with async/await support
- Local PDB file storage and parsing capabilities
Setup
- Install dependencies:
uv sync
- Configure environment variables in
.env:
PDB_MCP_HOST=localhost
PDB_MCP_PORT=8080
Available Tools
Core Data
structural_assembly_description: Get assembly structureschemical_component: Get chemical component detailspolymer_entity: Get polymer entity informationstructure: Get structure details
Annotations
drugbank_annotations: DrugBank data for compoundsuniprot_annotations: UniProt protein annotationspubmed_annotations: PubMed literature references
Repository Info
current_entry_ids: List current PDB entriesstructure_status: Check entry statusunreleased_structures: Get unreleased structure info
Docker Usage
Run with Docker Compose:
docker compose up pdb-server
The server will be available at http://localhost:8080.
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