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pyaptamer - AI for aptamer discovery

sponsored by ecoSPECS

The python library for easy aptamer design.

Tutorials · Issue Tracker · Project Board
Open Source BSD 3-clause GC.OS Sponsored
Community !discord !slack
CI/CD github-actions
Code !pypi !python-versions !black

🌟 Features

  • ✅ aptamer design and optimization algorithms
  • ✅ feature extraction from proteins and compounds
  • ✅ compatible with pdb and biopython
  • ✅ scikit-learn-like API - standardized and composable
  • 🛠️ Easily extendable with plugins
  • 📦 Minimal dependencies

NOTE: the package is in early development, API is unstable and not 100% features are complete - contributions appreciated!

🛠️ Usage

Checkout examples/ to see how to use the current API.

⚡ Installation

PyPI prerelease

pip install pyaptamer==0.1.0a1

NOTE: pyaptamer is in early development. The API is unstable and may change between releases.

Development install

# Clone the repository
git clone https://github.com/gc-os-ai/pyaptamer.git

# Install dependencies
pip install -e .  # latest version
# or editable developer install
pip install -e ".[dev]"

🤝 Contributing

Contributions are welcome! 🎉

How to start: find a good first issue

and/or join the discord and ping the developers, you can also ask for longer projects here.

Please open an issue before making a PR about bug/feature.

Contributions and participation are subject to the GC.OS Code of Conduct.

🗺️ Roadmap

  • more complete set of aptamer design and protein feature algorithms
  • wider support for cif and/or biopandas
  • integration of first-principles simulation tools
  • Community feedback integration - suggest features on the issue tracker!

Team

The package is maintained in collaboration between ecoSPECS and the German Center for Open Source AI.