About Me

Hey there! I am Inken Fender and I develop and apply computational methods to understand biological processes (with a focus on predicting protein-ligand interactions). My research includes all-atom molecular dynamics (MD), deep learning (DL), and natural language processing (NLP). I am passionate about using computation to predict biological outcomes furthering our understanding of biology as well as exploring the limits of computational models.

Background

I studied Biochemistry in my Bachelor's in Tübingen, then went to study Bioinformatics at the University of Hamburg. Currently, I am doing my PhD studies in Computational Biology, this time in beautiful switzerland, at the University of Bern in the research group of Prof. Dr. Thomas Lemmin.

Papers

2025

Beyond performance: how design choices shape chemical language models

I. Fender & J. Gut, T. Lemmin

We analysed the impact of design choices in chemical language models on their performance and internal representations. Check out our blog post to learn more.

2024

Structure and mechanism of a phosphotransferase system glucose transporter

P. Roth, J.-M. Jeckelmann, I. Fender, Z. Ucurum, T. Lemmin & D. Fotiadis

I ran and analysed all-atom molecular dynamics simulations. I performed the analysis of protein dynamics across multiple microsecond-scale simulations and communicated results interdisciplinary.

LifeSoaks image
2023

LifeSoaks: A tool for analyzing solvent channels in protein crystals and obstacles for soaking experiments

J. Pletzer-Zelgert, C. Ehrt, I. Fender, A. Griewel, F. Flachsenberg, G. Klebe & M. Rarey

I implemented and tested the integration of LifeSoaks into the ProteinsPlus web server.

Awards, recognitions, and representation

I care about representation. I got elected to be board member of the MVUB - the intermediate staff association at the University of Bern, and to be delegate of Actionuni (the umbrella organisation of all intermediate staff associations in Switzerland).

The Outstanding Degree Prize in Bioinformatics was awarded to me in 2022 in recognition of my master’s degree.

In 2018, a DAAD RISE scholarship allowed me to complete an internship abroad at the lab of Dr. Fabio Parmeggiani in Bristol.

Skills

Deep Learning, Biochemistry, Bioinformatics, Molecular Dynamics, Natural Language Processing

.. with Linux, Python, tcl, VMD, OpenMM

Interests

I’m passionate about computational biology, machine learning, and most things in science that can advance scientific research. Besides science, I do standard dancing, love swimming, laughing with friends, and exploring new places.