Michael Bakker · Bioinformatics & Pharmaceuticals
Understanding proteins
in motion.
I combine molecular simulations, quantum chemistry, and machine learning to investigate how protein dynamics shape biological function and disease.
Postdoctoral researcher · Charles University, Czech Republic
Pharmaceutical ModelingDisordered ProteinsMachine LearningPeptidomimetics
Research focus
Three main projects.
One pharmaceutical focus.
My current researches focuses on the areas of pharmacology which are either unattainable or unresolved in current research by focusing on the dark proteome, peptidomimetics and orphan nuclear receptors.
Intrinsic Disorder
How flexible regions of p53 and Tau respond to molecular context and chemical modifications.
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Orphan Nuclear Receptors
Investigating the interfaces and interactions that govern nuclear receptor function.
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Peptidomimetics
A current research focus connecting peptide-inspired molecular design with pharmaceutical modeling.
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Michael Bakker · Ph.D.
Let’s connect.
I’m a postdoctoral researcher at Charles University in the Czech Republic. Interested in protein dynamics or computational chemistry? Get in touch to discuss ideas and potential collaborations.
Featured research · p53
What can a flexible
protein region tell us?
My p53 research asks how the context around a disordered region changes the structures it can adopt, and how phosphorylation influences its dynamics.
Using molecular dynamics simulations, we investigate how neighboring domains constrain the pre-tetramerization loop. Comparing these simulated ensembles with experimental NMR chemical shifts helps assess how well the models capture its behavior.
Explore the p53 project →Selected work
From simulations
to published insights.
Physical Chemistry and Chemical Physics
Improving IDP theoretical chemical shift accuracy and efficiency through a combined MD/ADMA/DFT and machine learning approach
Notes from the workflow
Writing & tools.
November 2025
Coarse-Grained Modeling - A Quick Guide
Read article →November 2025
Flexibility Matters: Challenges of Binding Disordered Regions
Read article →PyMOL · Visualization tools
Give your prolines
some style.
Explore the visualization guide and download the accompanying PyMOL script.