PDB-MCP-Server and protein-mcp-server
Both projects are competing MCP servers providing access to protein structural data from the PDB, with the latter project also integrating data from PDBe and UniProt, and demonstrating significantly higher adoption.
About PDB-MCP-Server
Augmented-Nature/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.
Exposes PDB search, structure retrieval, and quality validation through five core tools and URI-based resources, enabling direct access to multiple coordinate formats (PDB, mmCIF, mmTF, XML) and validation metrics like resolution, R-factors, and clash scores. Integrates with RCSB PDB's REST, Search, and File Download APIs via stdio transport for seamless integration with Claude Desktop and complementary servers like UniProt and AlphaFold MCP. Implements comprehensive error handling for API rate limiting, invalid identifiers, and network failures.
About protein-mcp-server
cyanheads/protein-mcp-server
MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt.
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