Göttinger Graduiertenzentrum für Neurowissenschaften, Biophysik und Molekulare Biowissenschaften

de Groot, Bert, Prof. Dr.


  • 1998 PhD in Biophysical Chemistry, University of Groningen, the Netherlands
  • 1994 – 1998 PhD student, Lab of Prof. H.J.C. Berendsen, University of Groningen, the Netherlands
  • 1994 Degree in Chemistry, University of Groningen, the Netherlands
  • 1989 – 1994 Chemistry studies, University of Groningen, the Netherlands
  • 1998 – 2003 Postdoctoral Fellow, Theoretical Molecular Biophysics Group headed by Helmut Grubmüller, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
  • Since 2004 Head of the Computational Biomolecular Dynamics Research Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
  • 2009 Adjunct Professor Physics Faculty, Georg-August University, Göttingen, Germany
  • 2011 – 2017 Editorial Board Member, Biophysical Journal
  • Since 2013 Editorial Board Member, PLOS Computational Biology



Major Research Interests

Structure-dynamics-function relationships in proteins, studied by computational techniques. In particular: molecular mechanism of water and ion channels; the use of reduced dimensionality methods to analyse and accelerate MD simulations; MD and other simulation techniques for use in structure elucidation and refinement based on experimental data (x-ray, NMR, EM); development of alternative simulation approaches like the CONCOORD method.


Homepage Department/Research Group

http://www.mpibpc.mpg.de/groups/de_groot/




Selected Recent Publications



  • Gu RX and de Groot B . Central cavity dehydration as a gating mechanism of potassium channels. Nature Comm. 14: 2178 (2023).

  • Zhang Y, Daday C, Gu RX, Cox CD, Martinac B, de Groot B and Walz T. Visualization of the mechanosensitive ion channel MscS under membrane tension. Nature 590: 509-514 (2021)

  • Khalak Y, Tresadern G, Aldeghi M, Baumann HM, Mobley DL, de Groot B , Gapsys V. Alchemical absolute protein-ligand binding free energies for drug design Chemical Science 12: 13958-13971 (2021).

  • Gapsys V, Perez-Benito L, Aldeghi M, Seeliger D, van Vlijmen H, Tresadern G, de Groot B. Large scale relative protein ligand binding affinities using non-equilibrium alchemy. Chemical Science. 11: 1140-1152 (2020).

  • Kopec W, Rothberg BS, de Groot B. Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling. Nature Communications. 10: 5366 (2019).

  • Kopec W, Köpfer DA, Vickery ON, Bondarenko AS, Jansen TLC, de Groot B, Zachariae U (2018) Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels. Nature Chemistry 10:813-820

  • Smith CA, Ban D, Pratihar S, Giller K, Paulat M, Becker S, Griesinger C, Lee D, de Groot B (2016) Allosteric switch regulates protein-protein binding through collective motion. Proc. Nat. Acad. Sci. 113:3269-3274

  • Gapsys V, Michielssens S, Seeliger D, de Groot B (2016) Accurate and rigorous prediction of the changes in protein free energies in a large-scale mutation scan. Angew. Chem. Int. Ed. 55: 7364-7368

  • Schewe M, Nematian-Ardestani E, Sun H, Musinszki M, Cordeiro S, Bucci G, de Groot B, Tucker SJ, Rapedius M, Baukrowitz T (2016) A Non-Canonical Voltage Sensor Controls Gating in K2P K+ Channels. Cell. 164: 937-949

  • Gapsys V, Michielssens S, Seeliger D, de Groot B (2015) pmx: Automated protein structure and topology generation for alchemical perturbations. J. Comput. Chem. 36:348-354

  • Köpfer DA, Song C, Gruene T, Sheldrick GM, Zachariae U, de Groot B (2014) Ion permeation in K+ channels occurs by direct Coulomb knock-on. Science 346: 352-355