Overview
The RCSB PDB Explorer MCP Server is an unofficial MCP server specialized in understanding and retrieving information from the RCSB Protein Data Bank (PDB). It enables AI models (e.g., Claude) to directly access PDB data to answer questions, bridging natural language queries with the PDB's structured data. Core capabilities include fetching details about specific PDB entries (such as experimental methods), retrieving information about molecules, sequences, and experimental data, and querying Computed Structure Models (CSMs). It leverages the PDB GraphQL API to perform targeted queries and returns structured results to the AI. The server can be used with Cloudflare's AI Playground or Claude Desktop, with example server URLs and configuration snippets provided in the README. For developers, the core logic is located in src/index.ts, and deployment guidance references Cloudflare's remote MCP demos. The project is MIT licensed with an Academic Citation Requirement, encouraging attribution in scholarly work.
Features
PDB entry details retrieval
Fetch detailed information for specific PDB entries, including experimental methods and related metadata.
Molecule, sequence, and experimental data access
Retrieve information about molecules, sequences, and associated experimental data from the PDB.
Query Computed Structure Models (CSMs)
Support querying Computed Structure Models to obtain model-based structural information.
Access via PDB GraphQL API
Power queries through the RCSB PDB GraphQL API to retrieve structured data for AI use.
Who Is This For?
- AI researchers:Leverage the MCP server to query PDB data within AI workflows and conversational assistants.
- bioinformaticians:Retrieve PDB details, molecules, sequences, and experimental data for analyses and research.
- developers / IT teams:Deploy and configure MCP server instances and integrate with tools like Cloudflare AI Playground or Claude Desktop.
