Swiss-Model Batch Processor

Automate Multi-Target Homology Modeling Using a Single Template with SwissModel API

Overview

Swiss-Model Batch Processor is a Python-based automation tool designed to batch submit multiple protein sequences to SwissModel using a single structural template. This script simplifies high-throughput homology modeling by programmatically handling job submissions, monitoring, and structured result retrieval.

Features

• Batch Submission – Automates SwissModel API requests for multiple sequences.
• Single Template Usage – Models all targets against one specified template.
• Parallel Processing – Uses multithreading for faster execution.
• Rate Limit Handling – Prevents exceeding SwissModel’s API limits (100/min, 2000/6h).
• Structured Output Management – Saves models in separate directories based on clusters.
• Separate PDB & CIF Outputs – Organizes PDB and CIF files into dedicated subfolders.
• GUI Interface - Provides a user-friendly GUI for easy usage.

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Installation

To use the GUI:

Download the Executable From the releases page:

• Windows: Download
• Linux: Download

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For the Python Script

1. Clone the Repository:

   git clone https://github.com/Aaryesh-AD/Swiss_Model_Batch_Processor.git
   cd Swiss_Model_Batch_Processor

2. Install any required dependencies (if not already installed).

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Setup

Step 1: Configure API Access

SwissModel requires an API Key for authentication. Follow these steps:

1. Retrieve your API Key/Token from the SwissModel Account Page.

2. For the python CLI usage, in the project directory, create a new file called config.json and add your API Key/Token:

   {
       "API_KEY": "your_api_key_here"
   }

For the GUI, the API key can be entered directly in the GUI.

Tip: Make sure config.json is kept secure and is not accidentally shared publicly.

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Step 2: Prepare Your Input Files

• FASTA File: A file containing the target sequences (in standard FASTA format) that you want to model.
• Template PDB File: The single template file (in PDB format) used as the structural basis for modeling all target sequences.

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Usage

There are two modes to run SwissBatchModeler: GUI and Command-Line Interface (CLI).

Using the GUI

• On Windows:
  Double-click on the Swiss-Modeler_Batch_Processor_GUI.exe file.

• On Linux:
  In the program directory, run:

  ./Swiss-Modeler_Batch_Processor_GUI

The GUI provides an interactive interface for selecting input files, configuring options, and viewing progress.

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Using the Python Script (CLI Mode)

Run the script with the following command:

python SM_batch_processor.py <fasta_file> <template_pdb_file> <output_directory>

Example:

python SM_batch_processor.py input.fasta template.pdb results/

Note: Ensure that the config.json file is located in the same directory as the script.

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Output Structure

Models are saved under output_directory/ in organized folders:

results/
├── cluster_0_model/
│   ├── PDB/
│   │   ├── cluster_0_model_001.pdb
│   │   ├── cluster_0_model_002.pdb
│   ├── CIF/
│   │   ├── cluster_0_model_001.cif
│   │   ├── cluster_0_model_002.cif
├── cluster_1_model/
│   ├── PDB/
│   │   ├── cluster_1_model_001.pdb
│   ├── CIF/
│   │   ├── cluster_1_model_001.cif
│   └── ...

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SwissModel API Details

• Authentication: Requires an API token in headers (Token {API_KEY}).
• Rate Limits:
  • Rapid Submission: 100 requests/minute
  • Prolonged Submission: 2000 requests/6 hours
• Endpoints:
  • Submit Job: POST https://swissmodel.expasy.org/user_template
  • Check Status: GET https://swissmodel.expasy.org/project/{project_id}/models/summary/

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Advanced Configuration

Modify batch settings in SM_batch_processor.py:

RAPID_RATE_LIMIT = 100  # Max 100 requests per minute
REQUEST_INTERVAL = 60   # 1-minute interval if rate is exceeded
MAX_WORKERS = 5         # Adjust thread count for parallel processing

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License

This project is licensed under the MIT License.

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Contributions

Contributions are welcome! To contribute:

1. Fork the repo.
2. Create a new branch (feature-name).
3. Commit changes and push.
4. Submit a pull request.

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Contact

For issues, please open a GitHub issue or contact adeshpande334@gatech.edu.

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References

1. Waterhouse A, et al. (2018)
   SWISS-MODEL: homology modelling of protein structures and complexes.
   Nucleic Acids Res 46, W296-W303.
   PubMed | DOI

2. Bienert S, et al. (2017)
   The SWISS-MODEL Repository - new features and functionality.
   Nucleic Acids Res 45, D313-D319.
   PubMed | DOI

3. Guex N, Peitsch MC, Schwede T (2009)
   Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective.
   Electrophoresis 30, S162-S173.
   PubMed | DOI

4. Studer G, et al. (2020)
   QMEANDisCo - distance constraints applied on model quality estimation.
   Bioinformatics 36, 1765-1771.
   PubMed | DOI

5. Bertoni M, et al. (2017)
   Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology.
   Scientific Reports 7.
   PubMed | DOI

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