How do I connect Pubchem MCP Server to Claude?

The listing records `docker run -p 3010:3010 pubchem-mcp-server` as its setup step. Run it, then follow the repository's instructions for the client configuration; the listing names Claude Desktop, Cursor, VS Code as compatible clients.

Is Pubchem MCP Server free?

The listed licence is Apache-2.0. Check the upstream terms for permitted use and commercial requirements; a public repository does not by itself mean the software is free or open source. Connected APIs and hosted services may have separate charges.

What can Pubchem MCP Server do?

Pubchem MCP Server documents 11 tools to the agent, including maxAtoms, pubchem_get_bioactivity, pubchem_get_compound_3d_structure. The descriptions above come from project documentation. A live handshake does not test individual tool behavior.

Pubchem MCP Server

Unclaimed

by cyanheads

Search the PubChem chemical database for compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP. STDIO or Streamable HTTP.

Install

$docker run -p 3010:3010 pubchem-mcp-server

Set up this server

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This server needs project-specific setup. Follow the project instructions; no reusable public launch command is available yet.

Project instructions

bioinformaticscheminformaticschemistrycyanheadsllm-toolsmcpmcp-serverpubchemscientific-computing

Is this your MCP server?

This listing was auto-indexed from the public record. Claim it to edit the page, set compatibility and unlock growth tools. Takes under two minutes.

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Security profile

Claimed and verified servers get a weekly static scan that shows what the code can reach: external services, environment variables, shell commands, agent configuration folders, plus any dependencies with known advisories. Claim this listing to get one. How the security profile works

11 of 11 tools

Documented tools (11)

From project documentation. A server handshake does not verify each tool’s description or behavior.

maxAtoms

/maxBonds bound the atom/bond preview and includeRawSdf opts into a large raw SDF past the safe line cap; atomCount/bondCount always report the totals and any capping is disclosed

pubchem_get_bioactivity

Get a compound's bioactivity profile: assay results, targets, and activity values; filter by outcome or molecular target.

pubchem_get_compound_3d_structure

Fetch a 3D conformer (atomic coordinates and bonds) for a compound by CID, as parsed JSON or raw SDF.

pubchem_get_compound_details

Get physicochemical properties, descriptions, synonyms, drug-likeness, and classification for compounds by CID.

pubchem_get_compound_image

Fetch a 2D structure diagram (PNG) for a compound by CID.

pubchem_get_compound_interactions

Get drug-drug, drug-food, and chemical-target interactions for a compound by CID.

pubchem_get_compound_safety

Get GHS hazard classification and safety data for one or more compounds by CID (batch).

pubchem_get_compound_xrefs

Get external database cross-references (PubMed, patents, genes, proteins, etc.).

pubchem_get_summary

Get summaries for PubChem entities: assays, genes, proteins, taxonomy.

pubchem_search_assays

Find bioassays by biological target (gene symbol, protein, Gene ID, UniProt accession).

pubchem_search_compounds

Search for compounds by name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity.

Tool change history

Compared across complete checks of the same configuration. Tools were listed, not invoked. Input-schema changes are not measured here.

No complete tool checks yet.

FAQ

Questions about Pubchem MCP Server

How do I connect Pubchem MCP Server to Claude?: The listing records `docker run -p 3010:3010 pubchem-mcp-server` as its setup step. Run it, then follow the repository's instructions for the client configuration; the listing names Claude Desktop, Cursor, VS Code as compatible clients.
Is Pubchem MCP Server free?: The listed licence is Apache-2.0. Check the upstream terms for permitted use and commercial requirements; a public repository does not by itself mean the software is free or open source. Connected APIs and hosted services may have separate charges.
What can Pubchem MCP Server do?: Pubchem MCP Server documents 11 tools to the agent, including maxAtoms, pubchem_get_bioactivity, pubchem_get_compound_3d_structure. The descriptions above come from project documentation. A live handshake does not test individual tool behavior.