About Me

I’m an assistant professor of Digital Life Sciences at the HES-SO Valais-Wallis (University of Applied Sciences of Western Switzerland) and develop methods for design of novel proteins and open science tools for the life sciences.

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Interests
  • Optimization of biocatalysts using molecular modelling and deep learning
  • De novo design of functional proteins
  • Lab-in-the-loop approaches and the use of AI agents for lab automation
  • Scientific data visualization
  • Scientific illustrations using web technologies
Education

  • PhD Protein Design

    EPFL

  • MSc Life Science

    University of Konstanz

  • BSc Life Science

    University of Konstanz

📚 My Research
I have published state-of-the-art deep learning models for modelling metal cofactors in proteins (Metal3D/AllMetal3D) and collaborated with researchers at Stanford to use these algorithms to design novel metalloproteins (EVOLVE-M). I have also extensive experience in modelling of proteins using classical methods (e.g. molecular dynamics simulations) and high-level quantum mechanical molecular mechanical (QM/MM) simulations for the purpose of engineering enzymes by understanding ligand binding, tunnel formation and enzymatic catalysis. Please reach out to collaborate.
Featured Publications
AllMetal3D
Predicting metal-protein interactions using cofolding methods: Status quo
Metal3D: a general deep learning framework for accurate metal ion location prediction in proteins
Recent Publications
Simon Dürr (2025). AllMetal3D. AllMetal3D.
PDF Code Dataset DOI Huggingface
Simon Dürr, Ursula Rothlisberger (2024). Predicting metal-protein interactions using cofolding methods: Status quo. ML4LMS.
PDF Cite Dataset Poster
Simon Dürr, Andrea Levy, Ursula Rothlisberger (2023). Metal3D: a general deep learning framework for accurate metal ion location prediction in proteins. Nature Comms.
PDF Cite Code Dataset
Recent & Upcoming Talks
How to ... graphical abstracts?
Recent News

Review DisDock

Recently, the authors Menghan Lin, Keqiao Li, Yuan Zhang, Feng Pan, Wei Wu and Jinfeng Zhang at Florida State University reported a new tool called DisDock for predicting where metals bind in proteins.

From folder with files to archived and versioned public repository with DOI

For novices to git and to open science practices it can be hard to navigate the myriad of tools that are present to host ones data in an open repository such as Zenodo. This tutorial is an adaptation of a manual that I prepared for my lab in my function as data manager. It explains how to turn a folder into a git repository, how to setup a remote repository such as github and how to push the data to zenodo. In addition, this explains how to use interactive notebooks with github in a webbrowser using the mybinder.org service.

Kajaking in the Stockholm archipelago close to Uppsala - Tour & Packlist

The Stockholms archipelago is a fantastic collection of small little islets (Skar in swedish) and some bigger islands. It is a fantastic weekend getaway from Uppsala or Stockholm on a sunny weekend and allows for a nice nature experience and amazing sunsets. This post contains a short packlist, instructions how to access the Roslagens skargard (which is the northern part of the archipelago) and a route proposition for a three day trip.

Setup of Mendeley with Biber/Latex and Texmaker - a short Tutorial

There exist a plethora of tools for reference managment. Many of them come with support for propietary software like Microsoft's Word. If one is writing in Latex there are some challenges in finding a good reference manager that suits oneself and to make it work automatically with Latex.