ChEMBL Query

Query ChEMBL database for bioactivity data on drug-like compounds.

When to Use

• Find compounds active against a protein target (target-based search)
• Get bioactivity profile for a molecule (molecule-based search)
• Find drugs for a disease indication (indication-based search)

Workflow

Use Case 1: Target-Based Compound Search

Find compounds with activity against a protein target.

from open_biomed.tools.tool_registry import TOOLS

tool = TOOLS["chembl_query"]

# Search by target name
results, _ = tool.run(
    query_type="target",
    target_name="EGFR",
    standard_type="IC50",
    standard_value_lte=100,  # nM
    limit=20
)

# Or search by UniProt ID
results, _ = tool.run(
    query_type="target",
    uniprot_id="P00533",
    standard_type="IC50",
    limit=20
)

Use Case 2: Molecule Bioactivity Profile

Get all known targets and activity data for a compound.

# Search by molecule name
results, _ = tool.run(
    query_type="molecule",
    molecule_name="imatinib",
    limit=50
)

# Or search by SMILES
results, _ = tool.run(
    query_type="molecule",
    smiles="CC(=O)Oc1ccccc1C(=O)O",
    limit=20
)

# Or search by ChEMBL ID
results, _ = tool.run(
    query_type="molecule",
    chembl_id="CHEMBL25",
    limit=20
)

Use Case 3: Disease/Indication-Based Drug Search

Find drugs studied for a specific disease.

# Find all drugs for diabetes
results, _ = tool.run(
    query_type="indication",
    disease="diabetes",
    limit=50
)

# Filter for approved drugs only (max_phase=4)
results, _ = tool.run(
    query_type="indication",
    disease="diabetes",
    max_phase=4,  # Approved drugs only
    limit=20
)

Expected Outputs

Score Interpretation

Activity Values

Clinical Phase

Parameters

Error Handling

Available Tools

See examples/basic_example.py for complete runnable examples.