SMILES Profiling
Turn one SMILES into a compact pharmacology profile.
Tool stack
| Tool | Use |
|---|
| ------ | ----- |
| SwissTargetPrediction | Predicted protein targets with probabilities |
| PubChem | Exact CID, synonyms, MW, XLogP, TPSA, HBD/HBA, rotatable bonds |
| ADMETlab 3.0 | ADMET flags, drug-likeness, toxicity sections |
| ChEMBL | Similarity hits, max phase, known mechanisms, target names |
| PK-Smart | Human and animal PK estimates (VDss, CL, t½, fu, MRT) |
Workflow
- Use the user-provided SMILES as-is unless it clearly needs cleanup.
- Normalize only obvious salts/counterions.
- Run SwissTargetPrediction for target hypotheses.
- Run PubChem for identity and physicochemical baseline.
- Run ADMETlab 3.0 for ADMET flags and drug-likeness.
- Run ChEMBL for similarity hits and mechanism context.
- Run PK-Smart last for PK estimates.
- Merge the outputs into one short report, preferring direct database evidence over predictions.
Preferred scripts
scripts/run_smiles_profile.py for the full report.scripts/run_smiles_smoke.py --cases for regression/benchmark runs.
Extraction notes
- SwissTargetPrediction: capture the top 5 targets, probabilities, and species.
- PubChem: capture CID, IUPAC name, synonyms, MW, XLogP, TPSA, HBD/HBA, and rotatable bonds.
- ADMETlab 3.0: capture the section list and any obvious toxicity/drug-likeness flags.
- ChEMBL: capture the similarity threshold, top hits, max phase, mechanism_of_action, and target name.
- PK-Smart: capture VDss, CL, t½, fu, MRT, and animal PK when available.
Handling edge cases
- Salts/mixtures: strip common counterions first.
- Invalid SMILES: fail cleanly, do not crash.
- Missing tools: continue with the remaining sources.
- PubChem miss: report the miss and continue.
- ChEMBL miss: automatically fall back from 90 → 80 → 70 similarity.
Output shape
SMILES: CC(=O)OC1=CC=CC=C1C(=O)O
## SwissTargetPrediction
- Top target: PTGS1 (prob: 0.76)
## PubChem
- CID: 2244 | Name: 2-acetyloxybenzoic acid
- MW: 180.16 Da | XLogP: 1.2 | TPSA: 63.6 Ų
## ADMETlab 3.0
- MW: 180.04 Da | QED: N/A
## ChEMBL
- Top hit: CHEMBL25 ASPIRIN | sim 100 | phase 4
- Mechanism: Cyclooxygenase inhibitor -> Cyclooxygenase
## PK-Smart
- VDss: 0.23 L/kg | CL: 10.41 mL/min/kg
- t½: 0.34 hr | fu: 0.67