pubchem-query
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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.
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