pubchem-mcp-server and PDB-MCP-Server

About pubchem-mcp-server

cyanheads/pubchem-mcp-server

A Model Context Protocol (MCP) server providing comprehensive LLM tools for the PubChem PUG REST API.

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.