PDB
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.
What is PDB?
PDB is a Model Context Protocol (MCP) server that allows AI assistants like Claude, Cursor, and VS Code to 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 assemb...
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.
This server falls under the Data Science & ML and Search & Data Extraction categories on MCPgee, the world's largest MCP server directory with 33,000+ servers.
Features
- A Model Context Protocol (MCP) server that provides access t
Use Cases
Maintainer
Works with
Installation
Manual Installation
npx pdb-mcp-serverConfiguration
Configuration Details
claude_desktop_config.json
Performance
Response Metrics
Resource Usage
How to Set Up and Use PDB
PDB MCP Server connects AI agents directly to the Protein Data Bank (PDB), the worldwide open-access repository of 3D structural data for proteins, nucleic acids, and molecular assemblies. Through this server, researchers and AI agents can search for structures by keyword or PDB ID, retrieve detailed metadata and quality metrics, download coordinate files in PDB/mmCIF/mmTF/XML formats, and cross-reference structures with UniProt accessions — all without leaving their AI client. It is particularly useful for drug discovery, structural bioinformatics, and computational biology workflows.
Prerequisites
- Node.js 18+ and npm installed
- An MCP-compatible client such as Claude Desktop or Claude Code
- Internet access to reach the RCSB PDB APIs (no API key required — PDB data is publicly accessible)
- Git to clone the repository (no npm package published separately)
Clone the repository
Clone the PDB MCP Server repository from GitHub.
git clone https://github.com/Augmented-Nature/PDB-MCP-Server
cd PDB-MCP-ServerInstall dependencies and build
Install npm dependencies and compile the TypeScript source to the build directory.
npm install
npm run buildAdd to Claude Desktop config
Configure the built server in your Claude Desktop MCP configuration, pointing to the compiled index.js.
{
"mcpServers": {
"pdb-server": {
"command": "node",
"args": ["/path/to/PDB-MCP-Server/build/index.js"]
}
}
}Verify the server is running
Optionally run the server in development mode to confirm it starts without errors before connecting your MCP client.
npm run devSearch and retrieve structures
Once connected, use the available tools to search structures by keyword, retrieve details by PDB ID, or download coordinate files.
PDB Examples
Client configuration
Claude Desktop configuration for the PDB MCP Server using the locally built Node.js binary.
{
"mcpServers": {
"pdb-server": {
"command": "node",
"args": ["/path/to/PDB-MCP-Server/build/index.js"]
}
}
}Prompts to try
Example prompts for querying protein structures through the PDB MCP server.
- "Search the Protein Data Bank for insulin structures and show me the top results"
- "Get detailed information about PDB structure 1HHO including resolution and experimental method"
- "Download the mmCIF coordinate file for PDB entry 6VXX"
- "Find all PDB structures linked to UniProt accession P00533 (EGFR)"
- "What is the validation quality score for PDB entry 7BV2?"Troubleshooting PDB
Build fails with TypeScript compilation errors
Ensure you are using Node.js 18+ and run npm install before npm run build. If errors persist, check that all devDependencies including TypeScript are installed by running npm install --include=dev.
Structure search returns no results for a known protein
The search_structures tool accepts PDB IDs (e.g., '1ABC'), protein names, or keywords. For specific IDs, use get_structure_info directly instead of search_structures for more reliable retrieval.
Claude Desktop does not show PDB tools after configuration
Verify the path in your config points to the compiled build/index.js (not src/). Run node /path/to/PDB-MCP-Server/build/index.js manually to confirm it starts without errors, then restart Claude Desktop.
Frequently Asked Questions about PDB
What is PDB?
PDB is a Model Context Protocol (MCP) server that 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. It connects AI assistants to external tools and data sources through a standardized interface.
How do I install PDB?
Follow the installation instructions on the PDB GitHub repository. Clone the repo, install dependencies, and add the server config to your AI client.
Which AI clients work with PDB?
PDB works with all major MCP-compatible AI clients including Claude Desktop, Claude Code, Cursor, VS Code (GitHub Copilot), Windsurf, and Cline.
Is PDB free to use?
Yes, PDB is open source and available under the NOASSERTION license. You can use it freely in both personal and commercial projects.
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