SwissTargetPrediction Batch Client

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Automate batch queries to SwissTargetPrediction using SMILES strings.
This Python script submits molecules, polls for results, and saves predictions to a CSV file.

Note: This tool is unofficial and not affiliated with the Swiss Institute of Bioinformatics (SIB). Please respect their server usage policies.

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✨ Features

• Submit multiple SMILES strings in batch
• Automatically poll for job completion (up to 30 seconds by default)
• Parse and save target prediction results with:
  • Target name
  • UniProt & ChEMBL IDs
  • Target class
  • Probability score
  • Known active compounds (3D/2D similarity)
• Save all results to a structured CSV file

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🛠️ Requirements

• Python 3.12+
• Required packages:

  pip install requests pandas lxml html5lib

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🚀 Usage

1. Clone or download this repository

2. Install dependencies

   pip install -r requirements.txt

3. Run the script

   python swiss_target_batch.py

   The default SMILES list is included for demo purposes. Replace it with your own:

   smiles_list = [
       "CC(=O)OC1=CC=CC=C1C(=O)O",  # Aspirin
       "CN1C=NC2=C1C(=O)N(C(=O)N2C)C",  # Caffeine
       # Add your SMILES here...
   ]

4. Results are saved to swiss_results.csv (configurable via output_csv parameter).

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⚠️ Important Notes

• Rate Limiting: The SwissTargetPrediction server may block or throttle frequent requests. The script includes a 2-second delay between submissions—do not remove it.
• Organism Support: Default is "Homo_sapiens". Supported values include:
  • "Homo_sapiens"
  • "Mus_musculus"
  • "Rattus_norvegicus"

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📄 Example Output (swiss_results.csv)

Target	Common name	Uniprot ID	ChEMBL ID	Target Class	Probability*	Known actives (3D/2D)	input_smiles
Cyclooxygenase-1	PTGS1	P23219	CHEMBL221	Oxidoreductase	0.756002348928	3 / 2	CC(=O)OC1=CC=CC=C1C(=O)O

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📜 License

This code is released under the ISC License.
The data and predictions are owned by SwissTargetPrediction / SIB.

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💡 Acknowledgments

• SwissTargetPrediction – a free web service for target prediction.
• Swiss Institute of Bioinformatics (SIB)

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🙏 Please cite the original SwissTargetPrediction paper if you use this in research!
Daina, A., Michielin, O., & Zoete, V. (2019). SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules. Nucleic Acids Research, 47(W1), W357–W364. https://doi.org/10.1093/nar/gkz382