Chembl MCP Server

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How to connect

Add it to any MCP client that supports remote servers.

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

7 tools

• 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…

• 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…

• 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…

• 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)…

• 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_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…

• 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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