Connect-MCP

io.github.cyanheads/chembl-mcp-server

io.github.cyanheads/chembl-mcp-server · v0.3.3

Link compounds to protein targets, rank bioactivity, and look up drug mechanisms and indications.

MCPremotelocal · npmno credentialsCRM & salesDatabases

Reported outcomes

No reports yet.

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

Last check

Reachable, 7 tools, protocol 2025-06-18 · checked 2026-10-17

Test & rating

B 80/100

What it does: 7 tools · 7 read, 0 write · Health, CRM & sales, Databases

Test call chembl_search_molecules: failed — tool error: Error: search_type=name requires a query. Recovery: Supply query for name/ID/InChIKey search, or structure (SMILES) wit (992 ms)

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: 0
  • 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://chembl.caseyjhand.com/mcp
Package
registry:   npm
identifier: @cyanheads/chembl-mcp-server
version:    0.3.3
transport:  stdio

Tools

7 tools listed at last check
  • chembl_search_molecules Discovery entry point for compounds. Find by name / ChEMBL ID / InChIKey with the default search_type=name (supply query), or run a structure search with search_type exact | similarity | substructure (supply structure as a SMILES). At least one of query or structure is required, and structure is req
  • chembl_get_bioactivities The flagship compound↔target bioactivity bridge: measurements for a molecule (target deconvolution / selectivity), a target (lead finding), or both together (how potently one compound hits one target). Supply at least one of molecule_chembl_id (from chembl_search_molecules) or target_chembl_id (from
  • chembl_search_targets Resolve a protein/gene/UniProt accession to the ChEMBL target ID that chembl_get_bioactivities needs for the target→leads workflow. Supply at least one of accession (UniProt, e.g. P00533), gene_symbol (e.g. EGFR), or query (free-text name); filter further by organism and target_type. Returns each ta
  • chembl_get_drug_info Pharmacology for a drug (molecule): mechanism(s) of action, the molecular target(s) it acts on, action type (inhibitor / agonist / …), first-approval year, and clinical indications with the max phase reached for each. Supply molecule_chembl_id (from chembl_search_molecules). Distinct from the openfd
  • chembl_get_assay Assay provenance behind a bioactivity row: description, type (binding / functional / ADMET / toxicity), the target it measures, organism, and ChEMBL's 1–9 confidence score (9 = direct assay on the protein target, lower = homologous or indirect). Supply assay_chembl_id from a chembl_get_bioactivities
  • chembl_dataframe_query Run a read-only SQL SELECT over the bioactivity rows chembl_get_bioactivities spilled to a canvas — rank, group, dedupe, and aggregate across the FULL set, not the inline preview. Reference each staged table by the name chembl_get_bioactivities returned — bioactivities for its potency_ranked view, b
  • chembl_dataframe_describe List the tables and columns staged on a canvas by chembl_get_bioactivities — inspect before calling chembl_dataframe_query to write correct SQL. Returns each table with its row count, kind (table | view), and column names + types. Requires CANVAS_PROVIDER_TYPE=duckdb.

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