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dr. ir. Anton Feenstra

Associate Professor, Faculty of Science, Bioinformatics

Associate Professor, AIMMS

Associate Professor, Research Programmes - Science, Integrative Bioinformatics

Personal information

I studied Molecular Life Sciences in Wageningen in the 1990's, and through one of my internships then landed a PhD project in Groningen on protein dynamics and folding. I didn't manage to solve the protein folding problem, and the topic expanded to long-term dynamics of biomolecules as that was actually tractable at the time. This lead me to post-doc work in toxicology, studying the dynamics of enzyme-ligand interactions and from there on to another post-doc in Bioinformatics on protein-protein interactions, before becoming an assistant, and recently associate professor. Since then, this has remained my major research focus.

Research

I am an Associate Professor of Structural Bioinformatics at Vrije Universiteit Amsterdam with over 20 years of experience in computational biology, protein structure, and systems bioinformatics. My research combines molecular dynamics, machine learning, and network modeling to understand protein-protein interactions and biological regulation. I have supervised multiple PhD students and postdocs, coordinated international collaborations, and contributed to widely used bioinformatics tools such as GROMACS and Praline.

My recent work includes the development of the PIPPEN family of deep learning protein language models (LLMs). These models encode predicted properties of protein sequences in numerical vectors, which can then be used for further analysis. In this project I will be contributing PIPPEN inference models and consulting on their implementation as it pretrains to the development of a coIP/MS classifier.

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