pubchem-mcp-server

pubchem-mcp-server

3.2

If you are the rightful owner of pubchem-mcp-server and would like to certify it and/or have it hosted online, please leave a comment on the right or send an email to henry@mcphub.com.

The PubChem MCP Server is a Model Context Protocol server that provides seamless integration with PubChem's chemical information database, enabling AI agents and scientific tools to access and analyze chemical data efficiently.

The PubChem MCP Server acts as a bridge between applications that understand the Model Context Protocol (MCP) and PubChem's extensive chemical database. It allows advanced AI assistants, IDE extensions, and custom research tools to interact directly with PubChem, automating chemical research and gaining insights without complex API integration. Built on the robust 'mcp-ts-template', this server ensures a standardized, secure, and efficient way to expose PubChem functionality via the MCP standard. By integrating with the PubChem PUG REST API, it provides comprehensive error handling and compliance with rate limits, making it an essential tool for AI-driven scientific research and discovery.

Features

  • Automated Chemical Research: Enables programmatic search for compounds, fetching detailed properties, and analyzing bioassay results.
  • Comprehensive PubChem Integration: Provides access to compound data, substance information, and bioassay metadata.
  • Advanced Search Capabilities: Supports search by identifier, structure, similarity, and molecular formula.
  • Secure and Efficient: Built with robust error handling, logging, and security features.
  • Image Generation: Fetches 2D structural images of compounds directly.

Tools

  1. pubchem_search_compound_by_identifier

    Searches for PubChem Compound IDs (CIDs) using a common chemical identifier.

  2. pubchem_fetch_compound_properties

    Fetches a list of specified physicochemical properties for one or more CIDs.

  3. pubchem_get_compound_image

    Fetches a 2D image of a compound's structure for a given CID.

  4. pubchem_search_compounds_by_structure

    Performs a structural search using a SMILES string or a CID as the query.

  5. pubchem_search_compounds_by_similarity

    Finds compounds with a similar 2D structure to a query compound.

  6. pubchem_search_compounds_by_formula

    Finds PubChem Compound IDs (CIDs) that match a given molecular formula.

  7. pubchem_fetch_substance_details

    Retrieves details for a given PubChem Substance ID (SID).

  8. pubchem_fetch_assay_summary

    Fetches a detailed summary for a specific PubChem BioAssay ID (AID).

  9. pubchem_search_assays_by_target

    Finds PubChem BioAssay IDs (AIDs) associated with a specific biological target.

  10. pubchem_fetch_compound_xrefs

    Fetches external cross-references (XRefs) for a given CID.