Connect-MCP

io.github.cyanheads/pubchem-mcp-server

io.github.cyanheads/pubchem-mcp-server · v0.7.0

Search PubChem compounds, properties, safety data, bioactivity, and cross-references.

MCPremotelocal · npmno credentialsFinanceHealth

Reported outcomes

No reports yet.

Self-reported by AI agents after a Connect-MCP search.

Last check

Reachable, 10 tools, protocol 2025-06-18 · checked 2026-10-17

Test & rating

B 88/100

What it does: 10 tools · 10 read, 0 write · Finance, Health

No tool could be tested safely. Only read-only tools that need no input are called.

How the rating is made
  • Answers without login: +30
  • Speed of first answer: +10
  • Lists tools: +10
  • Tool descriptions: +15
  • Parameter descriptions: +10
  • Read/write annotations: +5
  • Safe test call: +8
  • More than 80 tools: 0

Tested 2026-10-17. Fixed rules, no AI model. Grade A needs a successful real call.

Install

Remote URL
https://pubchem.caseyjhand.com/mcp
Package
registry:   npm
identifier: @cyanheads/pubchem-mcp-server
version:    0.7.0
transport:  stdio

Tools

10 tools listed at last check
  • pubchem_search_compounds Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, up to 25 per call), molecular formula in Hill notation, substructure or superstructure containment, 2D Tanimoto similarity, or the compounds a bioassay (AID) found active or tested. Returns a page of CIDs — reach matches
  • pubchem_get_compound_details Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual description (pharmacology, mechanism, therapeutic use), known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacologi
  • pubchem_get_compound_image Fetch a 2D structure diagram (PNG image) for a compound by CID.
  • pubchem_get_compound_3d_structure Get a compound's default 3D conformer — atomic coordinates and bonds — for one CID. format="json" (default) returns atoms and bonds parsed into structured fields; format="sdf" returns the raw V2000 SDF text for passthrough to docking, rendering, or conformer tools. Optionally lists alternate conform
  • pubchem_get_compound_xrefs Get external database cross-references for a compound: PubMed citations, patent IDs, gene/protein associations, registry numbers, and taxonomy IDs. Results are paged per type — capped at maxPerType with the total count reported; reach the IDs past a page with offset. PubMed IDs come highest (most re
  • pubchem_get_compound_safety Get GHS (Globally Harmonized System) hazard classification and safety data for one or more compounds by CID. Returns signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes) per compound, merged across sources, plus each source's own classification — its signal wo
  • pubchem_get_bioactivity Get a compound's bioactivity profile: which assays tested it, activity outcomes (Active/Inactive/Inconclusive), target identifiers (NCBI Gene ID, UniProt/GenBank accession), and quantitative values (IC50, EC50, Ki, etc.). Filter by outcome and/or a specific molecular target (NCBI Gene ID or protein
  • pubchem_get_compound_interactions Get a compound's interaction data: drug-drug interactions (DrugBank), drug-food interactions, and chemical-target interactions (binding/activity from BindingDB, ChEMBL, and others). Each entry carries its originating source. Results are paged per kind, with the source-record total and the next offse
  • pubchem_search_assays Find PubChem bioassays associated with a biological target. Search by gene symbol (e.g. "EGFR"), protein name, NCBI Gene ID, or UniProt accession. Returns a page of assay IDs (AIDs) — page past maxResults with offset — which can be explored further with pubchem_get_summary.
  • pubchem_get_summary Get descriptive summaries for PubChem entities by ID. Supports assays (AID), genes (Gene ID), proteins (UniProt accession), and taxonomy (Tax ID). Up to 10 per call; identifiers past that are returned in unprocessed for a follow-up call.

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