Access RCSB PDB Data via GraphQL
Access RCSB PDB data via GraphQL API for protein structure information with this MCP server.
Why it matters
Enable AI assistants to directly query the RCSB Protein Data Bank (PDB) database using a GraphQL API. Retrieve detailed protein structure information, experimental data, and computed models through conversational interfaces.
Outcomes
What it gets done
Query PDB entries for experimental methods and titles.
Extract molecular and sequence information.
Access computed structure models (CSMs).
Integrate PDB data into AI-driven research workflows.
Install
Add it to your toolbox
Run in your project directory:
curl -fsSL https://spark.entire.vc/get/vb-rcsb-pdb | bash Overview
RCSB PDB MCP Server
What it does
This MCP server provides AI assistants with direct access to the RCSB Protein Data Bank (PDB) database. It integrates with the GraphQL API to enable the retrieval of detailed protein structure data, experimental information, and computed structure models.
How it connects
Use this server when you need to bridge AI models with structured RCSB PDB data. It is ideal for querying specific PDB entries, extracting information about molecules and sequences, or accessing computed structure models through a conversational AI interface.
Source README
An MCP server that provides AI assistants with direct access to the RCSB Protein Data Bank (PDB) database of protein structures through GraphQL API integration, enabling retrieval of protein structure data, experimental information, and computed structure models.
Configuration
Claude Desktop
{
"mcpServers": {
"rcsb-pdb": {
"command": "npx",
"args": [
"mcp-remote",
"YOUR_RCSB_PDB_SERVER_URL_HERE"
]
}
}
}
Capabilities
- Retrieval of detailed information about specific PDB entries, including experimental methods
- Extraction of information about molecules, sequences, and experimental data
- Queries to computed structure models (CSMs)
- Direct access to PDB GraphQL API through conversational AI
- Bridge between AI models and structured RCSB PDB data
Usage Examples
What is the experimental method used for PDB entry 4HHB?
Get the title and experimental method for PDB ID 1EHZ
Fetch the abstract for PDB entry 2DRI
Notes
This server is designed for deployment on Cloudflare Workers. Users need the URL of the deployed server to connect to AI interfaces such as Cloudflare AI Playground or Claude Desktop. The main logic is located in src/index.ts. Available under the MIT license with a requirement for academic citation when used in research.
Discussion
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