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io.github.cyanheads/chembl-mcp-server

io.github.cyanheads/chembl-mcp-server · v0.4.0

Measured by MCP Station

Description written by the publisher, not verified

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

Connect

claude mcp add --transport http chembl-mcp-server https://chembl.caseyjhand.com/mcp

{
  "mcpServers": {
    "chembl-mcp-server": {
      "url": "https://chembl.caseyjhand.com/mcp"
    }
  }
}

Tools as reported by the server

• 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 staged on 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, bi
• 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.

Tool changes

• 2026-10-18: chembl_search_molecules, chembl_get_bioactivities, chembl_search_targets, chembl_get_drug_info, chembl_get_assay, chembl_dataframe_query, chembl_dataframe_describe
• 2026-10-16: chembl_search_molecules, chembl_get_bioactivities, chembl_search_targets, chembl_get_drug_info, chembl_get_assay, chembl_dataframe_query, chembl_dataframe_describe

Repository · JSON · Text for agents · Registry updated 2026-10-18