PubChem Query

Query PubChem database for drug discovery and chemistry applications.

When to Use

• Convert drug name to molecular structure (SMILES, SDF)
• Find similar compounds for lead optimization
• Query bioactivity data against protein targets
• Get compounds active in specific assays

Workflow

Use Case 1: Name/ID to Structure

from open_biomed.tools.tool_registry import TOOLS

tool = TOOLS["molecule_name_request"]
molecules, _ = tool.run("aspirin")
mol = molecules[0]
print(f"SMILES: {mol.smiles}")

Use Case 2: Similarity Search

from open_biomed.data import Molecule

query = Molecule.from_smiles("CC(=O)Oc1ccccc1C(=O)O")  # aspirin
tool = TOOLS["molecule_structure_request"]
molecules, _ = tool.run(molecule=query, threshold=0.85, max_records=10)
for mol in molecules:
    print(mol.smiles)

Use Case 3: Bioactivity Query

tool = TOOLS["pubchem_bioactivity"]

# Query 1: Get assays where compound was active
results, _ = tool.run(query_type="compound", cid=2244, aids_type="active")

# Query 2: Get compounds active in an assay
results, _ = tool.run(query_type="assay", aid=1195, cids_type="active")

# Query 3: Get assays targeting a gene
results, _ = tool.run(query_type="target", gene_symbol="PTGS2")

Expected Outputs

Query Type	Output
Name to Structure	Molecule object with SMILES, SDF file saved
Similarity Search	List of similar Molecule objects
Bioactivity (compound)	List of AIDs where compound was active/inactive
Bioactivity (assay)	List of CIDs active/inactive in the assay
Bioactivity (target)	List of AIDs targeting the gene

Score Interpretation

Similarity Threshold	Interpretation
> 0.90	Very similar, likely same scaffold
0.80-0.90	Similar, potential analogs
0.70-0.80	Moderately similar, scaffold hops possible

Error Handling

Error	Solution
Compound not found	Try alternative names or SMILES
No similar compounds	Lower threshold (min 0.70)
No bioactivity data	Compound may not be tested; try related compounds
Timeout	Reduce max_records or retry

Available Tools

Tool Name	Purpose
molecule_name_request	Name/CID to structure
molecule_structure_request	Similarity search
pubchem_bioactivity	Bioactivity queries

See examples/basic_example.py for complete runnable examples.