pyaptamer - AI for aptamer discovery

sponsored by ecoSPECS

The python library for easy aptamer design.

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🌟 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 and not 100% feature complete - contributions appreciated!

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🛠️ Usage

to be completed

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⚡ Installation

Stable version from pip

NOTE: the package is not released yet on pypi - install from repo instead (unstable version)

pip install pyaptamer

Latest unstable version

# 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]"

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🤝 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.

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

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🗺️ 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!

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Team

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

• German Center for Open Source AI
  • Franz Kiraly (@fkiraly) - primary point of contact (package)
  • Simon Blanke (@simonblanke)
• ecoSPECS
  • Dennis Kubiczek (@KubiczekD) - primary point of contact (domain/aptamers)
  • Fatih Yolcu (@fat1hy0)
  • Jakob Birke (@jabirke)
  • Kerstin Moser (@KerstinMoser)
• European Summer of Code contributors 2025
  • Matteo Pinna (@nennomp)
  • Satvik Mishra (@satvshr)
  • Siddharth (@siddharth7113)