aizymes 0.1.1

A modular enzyme design platform

AI.zymes

Welcome to the code repository for AI.zymes — a modular platform for evolutionary enzyme design.

AI.zymes integrates a suite of state-of-the-art tools for enzyme engineering, including:

• 🛠️ Protein design (e.g. RosettaDesign, ProteinMPNN, LigandMPNN)
• 🔮 Structure prediction (e.g. ESMFold, RosettaRelax, MD minimization)
• ⚡ Electrostatic Catalysis (e.g. FieldTools)

Built with modularity in mind, AI.zymes allows you to easily plug in new methods or customize workflows for diverse bioengineering goals — from enzyme evolution to structure-function exploration.

We are currently working on improving the accessibility of AI.zymes, including a full user manual and installation instructions. Stay tuned!

📥 Getting Started

We are actively looking for collaborators and enthusiastic users! If you're interested in using AI.zymes or exploring joint projects, please reach out — we'd love to hear from you:

Contact:
📧 Adrian Bunzel
Max Planck Institute for Terrestrial Microbiology

📝 Citation

If you use AI.zymes in your research, please cite:

AI.zymes – A Modular Platform for Evolutionary Enzyme Design

Lucas P. Merlicek, Jannik Neumann, Abbie Lear, Vivian Degiorgi, Moor M. de Waal, Tudor-Stefan Cotet, Adrian J. Mulholland, and H. Adrian Bunzel Angewandte Chemie International Edition 2025, https://doi.org/10.1002/anie.202507031, (accepted)

🛠️ Developer Notes

AI.zymes is currently not distributed as a Python package (e.g. via pip). To use the platform in your own scripts or Jupyter notebooks, you need to ensure the source directory is included in your Python module search path.

Add the following line to your .bashrc (or .bash_profile) to permanently include the source directory:

export PYTHONPATH="$PYTHONPATH:$HOME/AIzymes/src"

This ensures that Python can locate modules like AIzymes_015.py when importing:

from AIzymes_015 import *

[!NOTE] Replace $HOME/AIzymes/src with the actual path if you have cloned the repository elsewhere.

---

This project is in active development. Contributions, feedback, and collaborations are very welcome!