Michael Bakker, B.Sc., M.Sc., Ph.D.

I am a postdoctoral researcher at Charles University in the Czech Republic, working at the intersection of computational chemistry, structural biology, and machine learning. My research focuses on protein dynamics, intrinsically disordered regions, and molecular recognition.

Email · Google Scholar · ORCID

Education

• B.S. in Chemistry (cum laude), Missouri State University, 2018
• Minor in Mathematics, Missouri State University, 2020
• M.S. in Chemistry (magna cum laude), Missouri State University, 2020
• Ph.D in Bioorganic Chemistry (Specialization: Computational Chemistry), Charles University, 2025

Awards

• Dimitris N. Chorafas Prize, 2025
  • Awarded for outstanding doctoral research in engineering sciences, medicine, or natural sciences.
• Missouri State University Outstanding Inorganic Chemistry Student Award
  • Awarded for top performance and research in inorganic chemistry (2017-2020).
• Missouri State University Hypercube Award
  • Awarded to top performing students working with computer science-related chemistry for work on biodiesel fracking (2013-2017).

Research Experience and Internships

• Postdoctoral Research Fellow
  • Charles University, Hradec Králové, CZ, 01.2025-present
  • Project: “Understanding the binding patterns of orphan nuclear receptor NR2F6”.
  • Implemented computational models including molecular dynamics, alanine scanning, hierarchical clustering, and AlphaFold to derive binding affinities.
  • Supported by the Grant Agency of the Czech Republic (Project GACR 22-17931B).
• Visiting Researcher (Erasmus Traineeship)
  • Lund University, Lund, SE, 04.2023 - 09.2023
  • Research Trainee under the tutelage of Dr. Marie Skepö.
  • Gained skills in utilizing synchrotrons, SAXS, and circular dichroism.
  • Investigated the pre-tetramerization loop of p53 and co-authored a technique to analyze conformational flexibility by decomposing ensembles by radius of gyration.
• Doctoral Researcher (Grant Agency of Charles University)
  • Charles University, Hradec Králové, CZ, 01.2021 - 12.2023
  • Worked on project 344321: “Calculation of NMR spin-spin couplings for intrinsically disordered proteins”.
  • Focused on the proline-rich region of Tau and the effect of hyper-phosphorylation.
• Doctoral Researcher (Czech Science Foundation)
  • Charles University, Hradec Králové, CZ, 09.2020 - 12.2022
  • Worked on project 19-14886Y: “Reliable calculations and predictions of NMR chemical shifts for the structural characterization of phosphorylated intrinsically disordered proteins”.
  • Developed and published two new techniques for clustering and assessing conformational landscapes.
• Master’s Research
  • Missouri State University, Springfield, MO, 01.2017-04.2020
  • Thesis on the computational pyrolysis of biodiesel, and published a paper on a new technique for generating 3D printing models from 2D NMR chemical shift NOESY.

Work Experience

• ACT Lecturer
  • Charles University, Hradec Králové, CZ, 2025–2026
  • Taught practical classes on utilizing simple publicly available office tools for computations and data presentations.
• Fall/Spring Semester 2016: Organic Chemistry PASS Tutor
  • Missouri State University
  • Duties included: Conducted regular sessions throughout the week ranging from group to singular interactions and held pre-examination testing sessions before each exam, personally crafting practice tests to supplement the education.
  • Supervisor: Professor Matthew Siebert
• Fall 2015: MSU Computer Service Technician
  • Missouri State University
  • Duties included: Fixing computer problems, removing viruses, diagnosing Blackboard server issues, and other IT related problems.
  • Supervisor: Jeremy Henson

Computer Programming

• Expert proficiency in Molecular Dynamics simulations through GROMACS
• Advanced proficiency in data analysis, visualization, and scripting using Python (including packages for Machine Learning, Dimensionality Reduction, and Clustering)
• Advanced proficiency in Quantum Chemical calculations using Density Functional Theory (DFT) and the Adjustable-Density Matrix Assembler (ADMA) fragmentation approach
• Advanced proficiency in bash scripting

Publications

• Comparative analysis of drop mass variance for manual and automatic delivery of large-scale eye drop poultry vaccine ★

  Bakker, M., Vraníková, B., Duintjer Tebbens, E. J., & Šklubalová, Z. (2026). Comparative analysis of drop mass variance for manual and automatic delivery of large-scale eye drop poultry vaccine. Poultry Science, 105(11), 107159. https://doi.org/10.1016/j.psj.2026.107159

• Conformational flexibility and transient structure of the proline-rich domain in p53

  Berggren, A., Bakker, M., Fisher, H., & Skepö, M. (2026). Conformational flexibility and transient structure of the proline-rich domain in p53. Biophysical Journal, 125(8), 1914–1925. https://doi.org/10.1016/j.bpj.2026.03.024

• Reduced Binding of Tau(210-240) to BIN1: Phosphate Charges Prefer n-Src/Distal Loops over RT-Src Loops

  Gaffour, A., Bakker, M., Bera, K., & Pavlíková Přecechtělová, J. (2025). Reduced Binding of Tau(210-240) to BIN1: Phosphate Charges Prefer n-Src/Distal Loops over RT-Src Loops. Biophysical Journal, 124(21), 3800–3810. https://doi.org/10.1016/j.bpj.2025.09.037

• The discovery of a new nonbile acid modulator of Takeda G protein-coupled receptor 5: An integrated computational approach

  Salam, R., Bakker, M., Krutáková, M., Štefela, A., Pávek, P., Duintjer Tebbens, J., & Zitko, J. (2025). The discovery of a new nonbile acid modulator of Takeda G protein-coupled receptor 5: An integrated computational approach. Archiv der Pharmazie, 358(1), e2400423. https://doi.org/10.1002/ardp.202400423

• Exploring the Role of Globular Domain Locations on an Intrinsically Disordered Region of p53: A Molecular Dynamics Investigation ★

  Bakker, M. J., Sørensen, H. V., & Skepö, M. (2024). Exploring the Role of Globular Domain Locations on an Intrinsically Disordered Region of p53: A Molecular Dynamics Investigation. Journal of Chemical Theory and Computation, 20(3), 1423–1433. https://doi.org/10.1021/acs.jctc.3c00971

• Exploring the Functional Landscape of the p53 Regulatory Domain: The Stabilizing Role of Post-Translational Modifications. ★

  Bakker, M. J., Svensson, O., Sørensen, H. V., & Skepö, M. (2024). Exploring the Functional Landscape of the p53 Regulatory Domain: The Stabilizing Role of Post-Translational Modifications. Journal of Chemical Theory and Computation, 20(14), 5842–5853. https://doi.org/10.1021/acs.jctc.4c00570

• Deeper Insight of the Conformational Ensemble of Intrinsically Disordered Proteins

  Svensson, O., Bakker, M. J., & Skepö, M. (2024). Deeper Insight of the Conformational Ensemble of Intrinsically Disordered Proteins. Journal of Chemical Information and Modeling, 64(15), 6105–6114. https://doi.org/10.1021/acs.jcim.4c00941

• Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering ★

  Bakker, M. J., Gaffour, A., Juhás, M., Zapletal, V., Stošek, J., Bratholm, L. A., & Pavlíková Přecechtělová, J. (2024). Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering. Journal of Chemical Information and Modeling, 64(16), 6542–6556. https://doi.org/10.1021/acs.jcim.4c00809

• Atomistic Details of Methyl Linoleate Pyrolysis: Direct Molecular Dynamics Simulation of Converting Biodiesel to Petroleum Products ★

  Bakker, M. J., & Siebert, M. R. (2024). Atomistic Details of Methyl Linoleate Pyrolysis: Direct Molecular Dynamics Simulation of Converting Biodiesel to Petroleum Products. Energies, 17(10), 2433. https://doi.org/10.3390/en17102433

• Improving IDP theoretical chemical shift accuracy and efficiency through a combined MD/ADMA/DFT and machine learning approach ★

  Bakker, M. J., Mládek, A., Semrád, H., Zapletal, V., & Pavlíková Přecechtělová, J. (2022). Improving IDP theoretical chemical shift accuracy and efficiency through a combined MD/ADMA/DFT and machine learning approach. Physical Chemistry Chemical Physics, 24(44), 27678–27692. https://doi.org/10.1039/D2CP01638A

• 3D printed NMR spectra: From 1D and 2D acquisition to 3D visualization ★

  Bakker, M., Boyd, B., & Meints, G. A. (2019). 3D printed NMR spectra: From 1D and 2D acquisition to 3D visualization. Concepts in Magnetic Resonance Part A, 47A(1), e21470. https://doi.org/10.1002/cmr.a.21470

Talks

Utilizing Machine Learning Algorithms and Fragmentation Techniques to Probe Intrinsically Disordered Proteins‘ Phase Space with NMR Chemical Shifts

July 10, 2022

Talk at Innsbruck University, Innsbruck, Austria

Intrinsically Disordered Regions in p53 Tumor Suppressor Protein

August 06, 2023

Talk at European Biophisical Society Association (EBSA), Stockholm, Sweden

Teaching

• Organic Chemistry Tutor

  University Sponsored Tutoring · Missouri State University, Department of Chemistry · 2016

• Organic Chemistry Lab Instructor

  Lab Instructor · Missouri State University, Department of Chemistry · 2018

• ACT Lecturer

  Practical Classes · Charles University, Faculty of Pharmacy · 2025–2026

• Calculus and Statistics Teaching Assistant

  Teaching Assistant · Charles University, Faculty of Pharmacy, Department of Inorganic and Organic Chemistry · 2025–2026