aizymes 0.1.11

A modular enzyme design platform

AI.zymes

[!NOTE] We are happy to tailor AI.zymes to your system! Contact Adrian Bunzel for specific requests!

[!NOTE] The AIzymes_Manual.pdf contains all information to get started. The manual is still work in progess. Feel free to reach out if you have any specific questions.

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

AIzymes_Manual.pdf contains all information to get started with AI.zymes. 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

🛠️ Installation

Check AIzymes_Manual.pdf for detailed installation instructions.

Briefly, we recommend installing AI.zymes with pip.

pip install aizymes

To use AI.zymes in Python, import:

from aizymes import *

For code development, AI.zymes can also be cloned from the GitHub repository:

git clone https://github.com/bunzela/AIzymes.git

You can either create your own AI.zymes environment, or install all required packages in your existing environment.

cd AIzymes
# To build new environemnt
conda env create -f environment.yml --name AIzymes 
# Alternative to install packages in curent environemnt:
# conda env update -f environment.yml --prune

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

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AI.zymes is in active development! Contributions, feedback, and collaborations are very welcome! We are happy to assist you with geting AI.zymes to run on your systems.

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License: MIT-NC – non-commercial academic use only. Commercial use requires permission. See LICENSE.txt.