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PubChem

Enables AI agents and scientific tools to interact with PubChem's vast chemical information database via the Model Context Protocol.

About

The PubChem MCP Server acts as a crucial bridge, allowing applications that understand the Model Context Protocol (MCP) – such as advanced AI assistants (LLMs), IDE extensions, or custom research tools – to seamlessly and efficiently interact with PubChem's extensive chemical database. It abstracts the complexities of the PubChem PUG REST API, providing a standardized, secure, and rate-limited interface. This empowers AI agents to automate chemical research, retrieve detailed compound properties, find similar structures, analyze bioassay results programmatically, and integrate chemical insights into AI-driven scientific discovery workflows.

Key Features

  • Comprehensive PubChem PUG REST API integration with rate limiting
  • 0 GitHub stars
  • Advanced chemical search capabilities (identifier, structure, similarity, formula)
  • Retrieval of full compound properties, substance, and bioassay details
  • Generation of 2D compound structural images directly from CIDs
  • Robust error handling, logging, and input validation via Zod schemas

Use Cases

  • Automating chemical research and data retrieval for AI agents and LLMs
  • Integrating PubChem's database into AI-driven scientific discovery platforms
  • Enabling programmatic analysis of structure-activity relationships and bioassay data
PubChem MCP: AI Agent & Scientific Chemical Database Access