pubchem-query

Research

Query PubChem database for chemical structures, similar compounds, and bioactivity data. Use this skill when: (1) Converting drug name to molecular structure (SMILES, SDF), (2) Finding similar compounds for lead optimization, (3) Querying bioactivity data against protein targets, (4) Getting compounds active in specific assays.

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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.