1. Sönke Cordeiro, Rocio K. Finol-Urdaneta, David Köpfer, Anna Markushina, Jie Song, Robert J. French, Wojciech Kopec, Bert L. de Groot, Mario J. Giacobassi, Lee S. Leavitt, Shrinivasan Raghuraman, Russell W. Teichert, Baldomero M. Olivera, and Heinrich Terlau. Conotoxin κM-RIIIJ, a tool targeting asymmetric heteromeric Kv1 channels. Proc. Nat. Acad. Sci. in press (2019). [pdf]
  2. Petra Rovo, Colin A. Smith, Diego Gauto, Bert L. de Groot, Paul Schanda, and Rasmus Linser. Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques. J. Am. Chem. Soc. in press (2019). [pdf]
  3. Rodolfo Briones, Christian Blau, Carsten Kutzner, Bert L. de Groot and Camilo Aponte-Santamaria. GROmaρs: A GROMACS-Based Toolset to Analyze Density Maps Derived from Molecular Dynamics Simulations. Biophys. J. 116: 4-11 (2019). [pdf]
  4. Helmut Lutz, Vance Jaeger, Tobias Weidner, and Bert L. de Groot. Interpretation of Interfacial Protein Spectra with Enhanced Molecular Simulation Ensembles. J. Chem. Theory Comput. 15: 698-707 (2019). [pdf]
  5. Matteo Aldeghi, Bert L de Groot, Vytautas Gapsys. Accurate Calculation of Free Energy Changes upon Amino Acid Mutation. in Computational Methods in Protein Evolution. 19-47 (2019). [pdf]


  6. Matteo Aldeghi, Vytautas Gapsys, and Bert L. de Groot. Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation. ACS Cent. Sci. 4: 1708-1718 (2018). [pdf]
  7. Julian T Brennecke, Bert L de Groot. Quantifying Asymmetry of Multimeric Proteins. J. Phys. Chem. A 122:7924-7930 (2018). [pdf]
  8. Wojciech Kopec, David A. Köpfer, Owen N. Vickery, Anna S. Bondarenko, Thomas L.C. Jansen, Bert L. de Groot, Ulrich Zachariae Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels. Nature Chemistry 10:813-820 (2018). [pdf]
  9. Tomas Bastys, Vytautas Gapsys, Nadezhda T. Doncheva, Rolf Kaiser, Bert L. de Groot, Olga V Kalinina. Consistent prediction of mutation effect on drug binding in HIV-1 protease using alchemical calculations. J. Chem. Theor. Comput. in press (2018). [pdf]
  10. T. Michael Sabo, Vytautas Gapsys, Korvin F.A. Walter, R. Bryn Fenwick, Stefan Becker, Xavier Salvatella, Bert L. de Groot, Donghan Lee, Christian Griesinger. Utilizing dipole-dipole cross-correlated relaxation for the measurement of angles between pairs of opposing Cα-Cα bonds in anti-parallel β-sheets. Methods 138: 85-92 (2018). [pdf]
  11. Leonard P. Heinz, Wojciech Kopec, Bert L. de Groot and Rainer H. A. Fink. In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathways. Sci. Rep. 8: 6886 (2018). [pdf]
  12. Julian T. Brennecke and Bert L. de Groot. Mechanism of Mechanosensitive Gating of the TREK-2 Potassium Channel. Biophys. J. 114: 1336-1343 (2018). [pdf]
  13. Chaowei Shi, Yao He, Kitty Hendriks, Bert L. de Groot, Xiaoying Cai, Changlin Tian, Adam Lange, Han Sun. A single NaK channel conformation is not enough for non-selective ion conduction. Nature communications 9: 717 (2018). [pdf]


  14. Vytautas Gapsys, Bert L. de Groot. Alchemical Free Energy Calculations for Nucleotide Mutations in Protein-DNA Complexes. J. Chem. Theor. Comput. 13: 6275-6289 (2017). [pdf]
  15. Dirk Matthes, Vytautas Gapsys, Christian Griesinger, Bert L. de Groot. Resolving the atomistic modes of anle138b inhibitory action on peptide oligomer formation. ACS Chem. Neurosci. 8:2791-2808 (2017). [pdf]
  16. David Ban, Colin A. Smith, Bert L. de Groot, Christian Griesinger, Donghan Lee. Recent advances in measuring the kinetics of biomolecules by NMR relaxation dispersion spectroscopy. Arch. Biochem. Biophys. 628: 81-91 (2017). [pdf]
  17. Camilo Aponte-Santamaria, Gerhard Fischer, Petra Bath, Richard Neutze, Bert L. Groot. Temperature dependence of protein-water interactions in a gated yeast aquaporin. Sci. Rep. 7: 4016 (2017). [pdf]
  18. Jan-Philipp Machtens, Rodolfo Briones, Claudia Alleva, Bert L. de Groot, Christoph Fahlke. Gating Charge Calculations by Computational Electrophysiology Simulations. Biophys. J. 112: 1396-1405 (2017). [pdf]
  19. Patrick O. Saboe, Chiara Rapisarda, Shreyas Kaptan, Yu-Shan Hsiao, Samantha R. Summers, Rita De Zorzi, Danijela Dukovski, Jiaheng Yu, Bert L. De Groot, Manish Kumar, Thomas Walz. Role of Pore-Lining Residues in Defining the Rate of Water Conduction by Aquaporin-0. Biophys. J. 112: 953-965 (2017). [pdf]
  20. Vytautas Gapsys, Bert L de Groot. pmx Webserver: A User Friendly Interface for Alchemistry. J. Chem. Inf. Model. 57: 109-114 (2017). [pdf]
  21. Marcus B. Kubitzki, Bert L. de Groot and Daniel Seeliger. Protein dynamics: from structure to function. In: From Protein Structure to Function with Bioinformatics. pp. 393-425 (2017). [pdf]
  22. Rodolfo Briones, Camilo Aponte-Santamaria, Bert L de Groot. Localization and ordering of lipids around Aquaporin-0: Protein and lipid mobility effects Front. Physiol. 8: 124 (2017). [pdf]
  23. Jing Huang, Sarah Rauscher, Grzegorz Nawrocki, Ting Ran, Michael Feig, Bert L. de Groot, Helmut Grubmüller, Alexander D. MacKerell Jr. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat. Methods. 14:71-73 (2017). [pdf]


  24. Dirk Matthes, Vytautas Gapsys, Julian Tim Brennecke and Bert L. de Groot. An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase. Sci. Rep. 6: 33156 (2016). [pdf]
  25. Hüseyin Ilgü, Jean-Marc Jeckelmann, Vytautas Gapsys, Zöhre Ucurum, Bert L. de Groot, and Dimitrios Fotiadis. Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC. Proc. Nat. Acad. Sci. 113:10358-10363 (2016). [pdf]
  26. Rodolfo Briones, Conrad Weichbrodt, Licia Paltrinieri, Ingo Mey, Saskia Villinger, Karin Giller, Adam Lange, Markus Zweckstetter, Christian Griesinger, Stefan Becker, Claudia Steinem, and Bert L. de Groot. Voltage Dependence of Conformational and Subconducting States of VDAC-1 Dynamics. Biophys J. 111:1223-1234 (2016). [pdf]
  27. Mette Assentoft, Shreyas Kaptan, Hans Peter Schneider, Joachim W. Deitmer, Bert L. de Groot, and Nanna MacAulay. Aquaporin 4 as a NH3 Channel. J. Biol. Chem. 291: 19184-19195 (2016). [pdf]
  28. Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger and Bert L. de Groot. Accurate and rigorous prediction of the changes in protein free energies in a large-scale mutation scan. Angew. Chem. Int. Ed. 55: 7364-7368(2016). [pdf]
  29. Andreas Kirscht, Shreyas S. Kaptan, Gerd Patrick Bienert, Francois Chaumont, Poul Nissen, Bert L. de Groot, Per Kjellbom, Pontus Gourdon and Urban Johanson. Crystal Structure of an Ammonia Permeable Aquaporin. PLOS Biol. 14:e1002411 (2016). [pdf]
  30. Marco Singer Tatyana Krivobokova, Axel Munk, and Bert L. de Groot. Partial least squares for dependent data. Biometrika 103 351-362 (2016) [pdf]
  31. Colin A. Smith, David Ban, Supriya Pratihar, Karin Giller, Maria Paulat, Stefan Becker, Christian Griesinger, Donghan Lee and Bert L. de Groot. Allosteric switch regulates protein-protein binding through collective motion. Proc. Nat. Acad. Sci. 113:3269-3274 (2016). [pdf]
  32. Carsten Kutzner, David A. Köpfer, Jan-Philipp Machtens, Bert L. de Groot, Chen Song, Ulrich Zachariae. Insights into the function of ion channels by computational electrophysiology simulations. BBA Biomembranes 1858:1741-1752 (2016). [pdf]
  33. Marcus Schewe, Ehsan Nematian-Ardestani, Han Sun, Mariane Musinszki, Sönke Cordeiro, Giovanna Bucci, Bert L. de Groot, Stephen J. Tucker, Markus Rapedius and Thomas Baukrowitz. A Non-Canonical Voltage Sensor Controls Gating in K2P K+ Channels. Cell. 164: 937-949 (2016). [pdf]


  34. Shreyas Kaptan, Mette Assentoft, Hans Peter Schneider, Robert A. Fenton, Joachim W. Deitmer, Nanna MacAulay, and Bert L. de Groot. H95 is a pH-dependent gate in aquaporin 4. Structure. 23:2309-2318 (2015). [pdf]
  35. Sarah Rauscher, Vytautas Gapsys, Michal J. Gajda, Markus Zweckstetter, Bert L. de Groot, and Helmut Grubmüller. Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment. J. Chem. Theor. Comput. 11: 5513-5524 (2015). [pdf]
  36. Vytautas Gapsys, Raghavendran L. Narayanan, ShengQi Xiang, Bert L. de Groot, Markus Zweckstetter. Improved validation of IDP ensembles by one-bond Cα-Hα scalar couplings. J. Biomol. NMR. 63:299-307 (2015). [pdf]
  37. Rasmus Linser, Nicola Salvi, Rodolfo Briones, Petra Rovo, Bert L. de Groot, Gerhard Wagner. The membrane anchor of the transcriptional activator SREBP is characterized by intrinsic conformational flexibility. Proc. Nat. Acad. Sci. 112:12390-12395 (2015). [pdf]
  38. Carsten Kutzner, Szilard Pall, Martin Fechner, Ansgar Esztermann, Bert L. de Groot and Helmut Grubmüller. Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. J. Comp. Chem. 36:1990-2008 (2015). [pdf]
  39. Servaas Michielssens, Bert L. de Groot and Helmut Grubmüller. Binding Affinities Controlled by Shifting Conformational Equilibria: Opportunities and Limitations. Biophys. J. 108:2585-2590 (2015). [pdf]
  40. Jan-Philipp Machtens, Daniel Kortzak, Christine Lansche, Ariane Leinenweber, Petra Kilian, Birgit Begemann, Ulrich Zachariae, David Ewers, Bert L. de Groot, Rodolfo Briones and Christoph Fahlke. Mechanisms of Anion Conduction by Coupled Glutamate Transporters. Cell 160:542-553 (2015). [pdf]
  41. Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger, and Bert L. de Groot. pmx: Automated protein structure and topology generation for alchemical perturbations. J. Comput. Chem. 36:348-354 (2015). [pdf]
  42. Vytautas Gapsys, Servaas Michielssens, Jan Henning Peters, Bert L. de Groot, Hadas Leonov. Calculation of Binding Free Energies. Molecular Modeling of proteins: 2nd edition. Book Series: Methods in Molecular Biology 1215: 173-209 (2015). [pdf]
  43. Colin A. Smith, David Ban, Supriya Pratihar, Karin Giller, Claudia Schwiegk, Bert L. de Groot, Stefan Becker, Christian Griesinger, Donghan Lee Population Shuffling of Protein Conformations Angew. Chem. Int. Ed. 54:207-210 (2015). [pdf] [supplement pdf]


  44. David A. Köpfer, Chen Song, Tim Gruene, George M. Sheldrick, Ulrich Zachariae and Bert L. de Groot. Ion permeation in K+ channels occurs by direct Coulomb knock-on. Science 346: 352-355 (2014). [pdf] [supplement pdf]
  45. Servaas Michielssens, Jan Henning Peters, David Ban, Supriya Pratihar, Daniel Seeliger, Monika Sharma, Karin Giller, Thomas Michael Sabo, Stefan Becker, Donghan Lee, Christian Griesinger and Bert L. de Groot. A Designed Conformational Shift To Control Protein Binding Specificity Angew. Chem. Int. Ed. 53: 10367-10371 (2014). [pdf] [supplement pdf]
  46. Dirk Matthes, Venita Daebel, Karsten Meyenberg, Dietmar Riedel, Gudrun Heim, Ulf Diederichsen, Adam Lange, Bert L. de Groot. Spontaneous Aggregation of the Insulin-Derived Steric Zipper Peptide VEALYL Results in Different Aggregation Forms with Common Features. J. Mol. Biol. 426: 362-376 (2014). [pdf]
  47. Jochen S. Hub, Bert L. de Groot, Helmut Grubmüller, and Gerrit Groenhof. Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge J. Chem. Theor. Comput. 10:381-390 (2014). [pdf]


  48. Licia Paltrinieri, Marco Borsari, Gianantonio Battistuzzi, Marco Sola, Christopher Dennison, Bert L. de Groot, Stefano Corni, and Carlo Augusto Bortolotti. How the Dynamics of the Metal-Binding Loop Region Controls the Acid Transition in Cupredoxins. Biochemistry 52: 7397-7404 (2013). [pdf]
  49. ShengQi Xiang, Vytautas Gapsys, Hai-Young Kim, Sergey Bessonov, He-Hsuan Hsiao, Sina Möhlmann, Volker Klaukien, Ralf Ficner, Stefan Becker, Henning Urlaub, 7, Reinhard Lürmann, Bert de Groot, Markus Zweckstetter. Phosphorylation Drives a Dynamic Switch in Serine/Arginine-Rich Proteins. Structure. 21: 2162-2174 (2013). [pdf]
  50. Vytautas Gapsys, Bert L. de Groot, Rodolfo Briones. Computational analysis of local membrane properties. J. Comput. Aided Mol. Des. 27: 845-858 (2013). [pdf]
  51. Martin Vesper and Bert L. de Groot. Collective Dynamics Underlying Allosteric Transitions in Hemoglobin. PLoS Comp. Biol. 9: e1003232 (2013). [pdf]
  52. Mette Assentoft, Shreyas Kaptan, Robert A. Fenton, Susan Z. Hua, Bert L. Groot, Nanna MacAulay. Phosphorylation of rat aquaporin-4 at Ser111 is not required for channel gating Glia 61: 1101-1112 (2013) [pdf]
  53. Tobias Linder, Bert L. de Groot and Anna Stary-Weinzinger. Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA. PLOS Comp. Biol. 9: e1003058 (2013). [pdf]
  54. Sören J. Wacker, Camilo Aponte-Santamaria, Per Kjellbom, Soren Nielsen, Bert L. de Groot, Michael Rützler. The identification of novel, high affinity AQP9 inhibitors in an intracellular binding site. Molec. Membrane Biol. 30:246-260 (2013). [pdf]
  55. Chen Song, Conrad Weichbrodt, Evgeniy S. Salnikov, Marek Dynowski, Björn O. Forsberg, Burkhard Bechinger, Claudia Steinem, Bert L. de Groot, Ulrich Zachariae, and Kornelius Zeth. Crystal structure and functional mechanism of a human antimicrobial membrane channel Proc. Nat. Acad. Sci. 110: 4586-4591 (2013). [pdf]
  56. Vytautas Gapsys and Bert L. de Groot. Optimal superpositioning of flexible molecule ensembles. Biophys. J. 104:196-207 (2013). [pdf] [supplement pdf]
  57. Daniel Seeliger, Cinta Zapater, Dawid Krenc, Rose Haddoub, Sabine Flitsch, Eric Beitz, Joan Cerda and Bert L. de Groot. Discovery of Novel Human Aquaporin-1 Blockers. ACS Chem. Biol. 8:249-256 (2013). [pdf] [supplement pdf]


  58. Guillem Portella, Tanja Polupanow, Florian Zocher, Danila A. Boytsov, Design of peptide-membrane interactions to modulate single-file water transport through modified gramicidin channels. Biophys. J. 103: 1698-1705 (2012). [pdf]
  59. Jan-Henning Peters and Bert L. de Groot. Ubiquitin dynamics in complexes reveal molecular recognition mechanisms beyond induced fit and conformational selection. PLOS Comp. Biol. 8: e1002704 (2012). [pdf]
  60. Tatyana Krivobokova, Rodolfo Briones, Jochen S. Hub, Axel Munk and Bert L. de Groot. Partial least squares functional mode analysis: application to the membrane proteins AQP1, Aqy1 and CLC-ec1. Biophys. J. 103:786-796 (2012). [pdf]
  61. David A. Köpfer, Ulrike Hahn, Iris Ohmert, Gert Vriend, Olaf Pongs, Bert L, de Groot, Ulrich Zachariae. A Molecular Switch Driving Inactivation in the Cardiac K+ Channel hERG. PLOS ONE. 7: e41023 (2012). [pdf]
  62. Ulrich Zachariae, Robert Schneider, Rodolfo Briones, Zrinka Gattin, Jean-Philippe Demers, Karin Giller, Elke Maier, Markus Zweckstetter, Christian Griesinger, Stefan Becker, Roland Benz, Bert L. de Groot, and Adam Lange. Beta-barrel mobility underlies closure of the voltage-dependent anion channel. Structure. 20:1540-1549 (2012). [pdf]
  63. Vytautas Gapsys, Daniel Seeliger, and Bert L. de Groot. New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations. J. Chem. Theor. Comput. 8:2373-2382 (2012). [pdf]
  64. Camilo Aponte-Santamaria, Rodolfo Briones, Andreas D. Schenk, Thomas Walz, Bert L. de Groot. Molecular driving forces defining lipid positions around aquaporin-0. Proc. Nat. Acad. Sci. 109: 44319-44325 (2012). [pdf]
  65. Sören J. Wacker, Wiktor Jurkowski, Katie J. Simmons, Colin W. G. Fishwick, Peter Johnson, David Madge, Erik Lindahl, Jean-Francois Rolland, Bert L. de Groot. Identification of Selective Inhibitors of the Potassium Channel Kv1.1-1.2(3) by High-Throughput Virtual Screening and Automated Patch Clamp. ChemMedChem 7:1775-1783 (2012). [pdf]
  66. Dirk Matthes, Vytautas Gapsys, Bert L. de Groot. Driving Forces and Structural Determinants of Steric Zipper Peptide Oligomer Formation Elucidated by Atomistic Simulations. J. Mol. Biol. 421:390-416 (2012). [pdf]
  67. Servaas Michielssens, Titus S. van Erp, Carsten Kutzner, Arnout Ceulemans, and Bert L. de Groot. Molecular Dynamics in Principal Component Space. J. Phys. Chem. B 116:8350-8354 (2012). [pdf]


  68. Sabina Jelen, Sören Wacker, Camilo Aponte-Santamaria, Martin Skott, Aleksandra Rojek, Urban Johanson, Per Kjellbom, Soren Nielsen, Bert L. de Groot, and Michael Rützler. Aquaporin-9 Protein Is the Primary Route of Hepatocyte Glycerol Uptake for Glycerol Gluconeogenesis in Mice J. Biol. Chem. 286: 44319-44325 (2011). [pdf]
  69. David Ban, Michael Funk, Rudolf Gulich, Dalia Egger, T. Michael Sabo, Korvin F.A. Walter, R. Bryn Fenwick, Karin Giller, Fabio Pichierri, Bert L. de Groot, Oliver F. Lange, Helmut Grubmüller, Xavier Salvatella, Martin Wolf, Alois Loidl, Reiner Kree, Stefan Becker, Nils-Alexander Lakomek, Donghan Lee, Peter Lunkenheimer, Christian Griesinger. Kinetics of Conformational Sampling in Ubiquitin. Angew. Chem. Int. Ed. 50:11437-11440 (2011). [pdf]
  70. Daniel Seeliger, Floris P. Buelens, Maik Goette, Bert L. de Groot and Helmut Grubmüller. Towards computional specificity screening of DNA-binding proteins. Nucleic Acids Res. 39: 8281-8290 (2011). [pdf]
  71. Carsten Kutzner, Helmut Grubmüller, Bert L. de Groot, Ulrich Zachariae. Computational Electrophysiology: The Molecular Dynamics of Ion Channel Permeation and Selectivity in Atomistic Detail. Biophys. J. 101: 809-817 (2011). [pdf]
  72. Lars Boukharta, Henrik Kernen, Anna Stary-Weinzinger, Gran Wallin, Bert L. de Groot, and Johan Aqvist. Computer Simulations of Structure-Activity Relationships for hERG Channel Blockers. Biochemistry. 50:6146-6156 (2011). [pdf]
  73. Jochen S. Hub and Bert L. de Groot. Comment on "Molecular Selectivity in Aquaporin Channels Studied by the 3D-RISM Theory." J. Phys. Chem. B. 115:8364-8366 (2011). [pdf]
  74. Dirk Matthes, Vytautas Gapsys, Venita Daebel and Bert L. de Groot. Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide Oligomerization. PLOS ONE. 6:e19129 (2011). [pdf]
  75. Bert L. de Groot and Jochen S. Hub. A Decade of Debate: Significance of CO2 Permeation through Membrane Channels still Controversial. ChemPhysChem. 12:1021-1022 (2011). [pdf]


  76. Saskia Villinger, Rodolfo Briones, Karin Giller, Ulrich Zachariae, Adam Lange, Bert L. de Groot, Christian Griesinger, Stefan Becker, Markus Zweckstetter. Functional dynamics in the voltage dependent anion channel. Proc. Nat. Acad. Sci. 107: 22546-22551 (2010). [pdf] [supplement pdf]
  77. Jochen S. Hub, Camilo Aponte-Santamaria, Helmut Grubmüller and Bert L. de Groot. Voltage-regulated water flux through aquaporin channels in silico. Biophys. J. 99:L97-L99 (2010). [pdf] [supplement pdf]
  78. Jochen S. Hub, Bert L. de Groot and David van der Spoel. g_wham - A free weighted histogram analysis implementation including robust error and autocorrelation estimates. JCTC. 6: 3713-3720 (2010). [pdf]
  79. J. J. Lopez Cascales, S. D. Oliviera Costa, Bert L. de Groot and D. Eric Walters. Binding of Glutamate to the Umami Receptor. Biophys. Chem. 152:139-144 (2010). [pdf]
  80. Jochen S. Hub, Fritz Winkler, Mike Merrick and Bert L. de Groot. Potentials of mean force and permeabilities for carbon dioxide, ammonia, and water flux across a Rhesus protein channel and lipid membranes. J. Am. Chem. Soc. 132:13251-13263 (2010). [pdf]
  81. Camilo Aponte-Santamaria, Jochen S. Hub and Bert L. de Groot. Dynamics and energetics of solute permeation through the Plasmodium falciparum aquaglyceroporin. PCCP. 12:10246-10254 (2010). [pdf]
  82. Oliver F. Lange, David van der Spoel and Bert L. de Groot. Scrutinizing Molecular Mechanics Force Fields on the Microsecond Timescale With NMR Data. Biophys. J. 99:647-655 (2010). [pdf] [supplement pdf]
  83. Daniel Seeliger and Bert L. de Groot. Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J. Computer-aided Molec. Design. 24:417-422 (2010). [pdf]
  84. Jochen S. Hub, Marcus Kubitzki and Bert L. de Groot. Spontaneous quaternary and tertiary T-R transitions of human hemoglobin in molecular dynamics simulation. PLOS Comput. Biol. 6:e1000774 (2010). [pdf]
  85. Daniel Seeliger and Bert L. de Groot. Protein thermostability calculations using alchemical free energy simulations. Biophys. J. 98:2309-2316 (2010). [pdf] [supplement pdf]
  86. Anna Stary, Sören Wacker, Lars Boukharta, Ulrich Zachariae, Yasmin Karimi-Nejad, Johan Aqvist, Gert Vriend and Bert L. de Groot. Toward a consensus model of the hERG potassium channel. ChemMedChem. 5:455-467 (2010). [pdf]
  87. Daniel Seeliger and Bert L. de Groot. Conformational transitions upon ligand binding: Holo structure prediction from apo conformations. PLOS Comput. Biol. 6: e1000634 (2010).[pdf]
  88. R. A. Fenton, H. B. Moeller, S. Nielsen, B. L. de Groot, and M. Rützler. A plate reader-based method for cell water permeability measurement. Am. J. Physiol. Renal Physiol. 298: F224-F230 (2010).[pdf]
  89. Teun P. de Boer, Lukas Nalos, Anna Stary, Bart Kok, Marien J.C. Houtman, Gudrun Antoons, Toon A.B. van Veen, Jet D.M. Beekman, Bert L. de Groot, Tobias Opthof, Martin B Rook, Marc A. Vos and Marcel A.G. van der Heyden. The antiprotozoic drug pentamidine blocks Kir2.x-mediated inward rectifier current by entering the cytoplasmic pore region. Br. J. Pharmacol. 159:1532-1541 (2010). [pdf]


  90. Jochen S. Hub and Bert L. de Groot. Detection of functional modes in protein dynamics. PLOS Comput. Biol. 5: e1000480 (2009).[pdf]
  91. Dirk Matthes and Bert L. de Groot. Secondary structure propensities in peptide folding simulations: A systematic comparison of molecular mechanics interaction schemes. Biophys. J. 97:599-608 (2009).[pdf] [supplement pdf]
  92. Christian M. Stegmann, Daniel Seeliger, George M. Sheldrick, Bert L. de Groot and Markus Wahl. Thermodynamic signature of trapped water molecules in a protein-ligand interaction. Angew. Chem. Int. Ed. 48:5207-5210 (2009).[pdf]
  93. Gerhard Fischer, Urszula Kosinska-Eriksson, Camilo Aponte-Santamaria, Madelene Palmgren, Cecilia Geijer, Kristina Hedfalk, Stefan Hohmann, Bert L. de Groot, Richard Neutze, Karin Lindkvist-Petersson. Crystal Structure of a Yeast Aquaporin at 1.15A Reveals a Novel Gating Mechanism. PLOS Biol. 7: e1000130 (2009).[pdf]
  94. Marcus B. Kubitzki, Bert L. de Groot and Daniel Seeliger. Protein dynamics: from structure to function. In: From Protein Structure to Function with Bioinformatics. pp. 217-249 (2009).[pdf]
  95. Jochen S. Hub, Helmut Grubmüller and Bert L. de Groot. Dynamics and Energetics of Permeation Through Aquaporins. What Do We Learn from Molecular Dynamics Simulations? In: Handbook of Experimental Pharmacology. Aquaporins. Vol. 190: 57-76 (2009). [pdf]
  96. Alexander Benedix, Caroline M. Becker, Bert L. de Groot, Amedeo Caflisch, Rainer A. Böckmann. Predicting Free Energy Changes Using Structural Ensembles. Nat. Methods. 6: 3-4 (2009).[pdf]
  97. Harshad V. Joshi, Mark J. Jedrzejas and Bert L. de Groot. Domain motions of hyaluronan lyase underlying processive hyaluronan translocation. Proteins. 76:30-46 (2009).[pdf]
  98. Guillem Portella and Bert L. de Groot. Determinants of water permeability through nanoscopic hydrophilic channels. Biophys. J. 96:925-938 (2009).[pdf] [new & notable pdf]
  99. Daniel Seeliger and Bert L. de Groot. tCONCOORD-GUI: Visually Supported Conformational Sampling of Bioactive Molecules. J. Comp. Chem. 30:1160-1166 (2009). [pdf]


  100. Nils-Alexander Lakomek, Oliver F. Lange, Korvin F.A. Walter, Christophe Fares, Dalia Egger, Peter Lunkenheimer, Jens Meiler, Helmut Grubmüller, Stefan Becker, Bert L. de Groot and Christian Griesinger. Residual dipolar couplings as a tool to study molecular recognition of ubiquitin. Biochem. Soc. Trans. 36: 1433-437 (2008).[pdf]
  101. Rainer A. Böckmann, Bert L. de Groot, Sergej Kakorin, Eberhard Neumann, Helmut Grubmüller. Kinetics, Statistics, and Energetics of Lipid Membrane Electroporation Studied by Molecular Dynamics Simulations. Biophys. J. 95: 1837-1850 (2008).[pdf]
  102. Guillem Portella, Jochen S. Hub, Martin D. Vesper, and Bert L. de Groot. Not only enthalpy: large entropy contribution to ion permeation barriers in single-file channels. Biophys. J. 95: 2275-2282 (2008).[pdf]
  103. Oliver F. Lange, Nils-Alexander Lakomek, Christophe Fares, Gunnar F. Schröder, Korvin F. A. Walter, Stefan Becker, Jens Meiler, Helmut Grubmüller, Christian Griesinger and Bert L. de Groot. Recognition dynamics up to microseconds revealed from RDC derived ubiquitin ensemble in solution. Science. 320:1471-1475 (2008). [pdf] [supplement pdf] [perspective pdf]
  104. Nils-Alexander Lakomek, Korvin F. A. Walter, Christophe Fares, Oliver F. Lange, Bert L. de Groot, Helmut Grubmüller, Rafael Brüschweiler, Axel Munk, Stefan Becker, Jens Meiler and Christian Griesinger. Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics J. Biomol. NMR. 41: 139-155 (2008).[pdf]
  105. Marcus B. Kubitzki and Bert L. de Groot. The Atomistic Mechanism of Conformational Transition in Adenylate Kinase: a TEE-REX Molecular Dynamics Study. Structure. 8:1175-1182 (2008).[pdf]
  106. Ulrich Zachariae, Robert Schneider, Phanindra Velisetty, Adam Lange, Daniel Seeliger, Sören J. Wacker, Yasmin Karimi-Nejad, Gert Vriend, Stefan Becker, Olaf Pongs, Marc Baldus and Bert L. de Groot. The molecular mechanism of toxin-induced conformational changes in a potassium channel: relation to C-type inactivation. Structure. 16:747-754 (2008).[pdf]
  107. Claudia Hartmann, Mohamed Chami, Ulrich Zachariae, Bert L. de Groot, Andreas Engel and Markus G. Grütter. Vacuolar protein sorting: Two different functional states of the AAA-ATPase Vps4p. J. Mol. Biol. 377:352-363 (2008).[pdf]
  108. Jochen S. Hub and Bert L. de Groot. Mechanism of selectivity in aquaporins and aquaglyceroporins Proc. Nat. Acad. Sci. 105:1198-1203 (2008).[pdf]
  109. Matthias E. Müller, Jochen S. Hub, Helmut Grubmüller and Bert L. de Groot. Is TEA an inhibitor for human Aquaporin-1? Pflugers Arch. 456:663-669 (2008).[pdf]


  110. Daniel Seeliger, Jürgen Haas, and Bert L. de Groot. Geometry-based Sampling of Conformational Transitions in Proteins. Structure 15: 1482-1492 (2007).[pdf]
  111. Jochen S. Hub, Tim Salditt, Maikel C Rheinstädter, and Bert L. de Groot. Short range order and collective dynamics of DMPC bilayers. A comparison between molecular dynamics simulations, x-ray, and neutron scattering experiments. Biophys. J. 93: 3156-3168 (2007).[pdf]
  112. Louic S. Vermeer, Bert L. de Groot, Valerie Reat, Alain Milon, Jerzy Czaplicki. Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments. Eur. Biophys. J. 36: 919-931 (2007). [pdf]
  113. Carsten Kutzner, David Van Der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. De Groot, Helmut Grubmüller. Speeding up parallel GROMACS on high-latency networks. J. Comp. Chem. 28:2075-2084 (2007). [pdf]
  114. Marcus B. Kubitzki and Bert L. de Groot. Molecular Dynamics Simulations using Temperature Enhanced Essential dynamics Replica EXchange (TEE-REX). Biophys. J. 92:4262-4270 (2007). [pdf]
  115. Guillem Portella, Peter Pohl and Bert L. de Groot. Invariance of Single-File Water Permeability in Gramicidin-like Peptidic Pores as function of Pore Length. Biophys. J. 92:3930-3937 (2007). [pdf]
  116. Daniel Seeliger and Bert L. de Groot. Atomic contacts in protein structures. A detailed analysis of atomic radii, packing and overlaps. Proteins. 68: 595-601 (2007). [pdf]


  117. S. Takamori, M. Holt, K. Stenius, E.A. Lemke, M. Grønborg, D. Riedel, H. Urlaub, S. Schenck, B. Brügger, Ph. Ringler, S.A. Müller, B. Rammner, F. Gräter, J. S. Hub, B.L. De Groot, G. Mieskes, Y. Moriyama, J. Klingauf, H. Grubmüller, J. Heuser, F. Wieland, and R. Jahn. Molecular Anatomy of a Trafficking Organelle. Cell 127:831-846 (2006). [pdf]
  118. Steven Hayward and Bert L. de Groot. Normal Modes and Essential Dynamics. in: Methods in molecular biology, vol 443, Molecular modelling of proteins 89-106 (2008). [pdf]
  119. Frauke Gräter, Bert L. de Groot, Hualiang Jiang and Helmut Grubmüller Ligand-Release Pathways in the Pheromone-Binding Protein of Bombyx mori Structure 14:1567-1576 (2006). [pdf]
  120. Jochen S. Hub and Bert L. de Groot. Does CO2 Permeate through Aquaporin-1? Biophys. J. 91:842-848 (2006). [pdf]
  121. Frank J. M. Detmers, Bert L. de Groot, E. Matthias Müller, Andrew Hinton, Irene B. M. Konings, Mozes Sze, Sabine L. Flitsch, Helmut Grubmüller, and Peter M. T. Deen. Quaternary Ammonium Compounds as Water Channel Blockers. J. Biol. Chem. 281:14207-14214 (2006). [pdf]
  122. Daniel Seeliger and Bert L. de Groot. Prediction of protein flexibility from geometrical constraints. Biotech International. 18:20-22 (2006). [pdf]
  123. Daniel J. Rigden, James E. Littlejohn, Harshad V. Joshi, Bert L. de Groot and Mark J. Jedrzejas. Alternate Structural Conformations of Streptococcus pneumoniae Hyaluronan Lyase: Insights into Enzyme Flexibility and Underlying Molecular Mechanism of Action. J. Mol. Biol. 358:1165-1178 (2006). [pdf]
  124. Sapar M. Saparov, Jochen R. Pfeifer, Loay Al-Momani, Guillem Portella, Bert L. de Groot, Ulrich Koert and Peter Pohl. Mobility of a One-Dimensional Confined File of Water Molecules as a Function of File Length. Phys. Rev. Lett. 96:148101 (2006). [pdf]
  125. J. B. Sørensen, K. Wiederhold, E. M. Müller, I. Milosevic, G. Nagy, B. L de Groot, H. Grubmüller, and D. Fasshauer. Sequential N- to C-terminal SNARE complex assembly drives priming and fusion of secretory vesicles. EMBO J. 25:955-966 (2006). [pdf]
  126. Bert L. de Groot, Rainer A. Böckmann, and Helmut Grubmüller. Proteindynamik-Simulationen. Molekulare Nanomaschinen unter der Lupe. Physik in unserer Zeit 37: 73-79 (2006). [pdf] [cover]


  127. Gabor Nagy, Ira Milosevic, Dirk Fasshauer, E. Matthias Müller, Bert L. de Groot, Thorsten Lang, Michael C. Wilson and Jakob B. Sorensen Alternative Splicing of SNAP-25 Regulates Secretion through Nonconservative Substitutions in the SNARE Domain Molecular Biology of the Cell 16: 5675-5685 (2005). [pdf]
  128. Heise H, Luca S, de Groot BL, Grubmüller H, Baldus M.; Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations. Biophys J. 89: 2113-2120 (2005). [pdf]
  129. W. Kukulski, A.D. Schenk, U. Johanson, T. Braun, B.L. de Groot, D. Fotiadis, P. Kjellbom and A. Engel; The 5 A Structure of Heterologously Expressed Plant Aquaporin SoPIP2;1. J. Mol. Biol. 350:611-616 (2005). [pdf]
  130. Andreas D. Schenk, Paul J.L. Werten, Simon Scheuring, Bert L. de Groot, Shirley A. Müller, Henning Stahlberg, Ansgar Philippsen and Andreas Engel;The 4.5 A Structure of Human AQP2 J. Mol. Biol. 350:278-289 (2005). [pdf]
  131. Oliver F. Lange, H. Grubmüller, and Bert L. de Groot; Molecular Dynamics Simulations of Protein G Challenge NMR-Derived Correlated Backbone Motions. Angew. Chem. Int. Ed. 44:3394-3399 (2005). [pdf]
  132. Bert L. de Groot and Helmut Grubmüller; The dynamics and energetics of water permeation and proton exclusion in aquaporins Curr. Opin. Struct. Biol. 15: 176-183 (2005). [pdf]


  133. B. L. de Groot and H. Grubmüller; Aquaporine: Die perfekten Wasserfilter der Zelle. BIOspektrum 4:384-386 (2004). [pdf]


  134. Bert L. de Groot, Tomaso Frigato, Volkhard Helms and Helmut Grubmüller; The mechanism of proton exclusion in the aquaporin-1 water channel. J. Mol. Biol. 333: 279-293 (2003). [pdf]
  135. Bert L. de Groot, Andreas Engel, and Helmut Grubmüller; The structure of the Aquaporin-1 water channel: a comparison between cryo-electron microscopy and x-ray crystallography. J. Mol. Biol. 325: 485-493 (2003). [pdf]


  136. P. J. L. Werten, H. -W. Remigy, B. L. de Groot, D. Fotiadis,A. Philippsen, H. Stahlberg, H. Grubmüller and A. Engel; Progress in the analysis of membrane protein structure and function.; FEBS Lett. 529:65-72 (2002). [pdf]
  137. Luciane V. Mello, Bert L. de Groot, Songlin Li, and Mark J. Jedrzejas; Structure and flexibility of streptococcus agalactiae hyaluronate lyase complex with its substrate: Insights into the mechanism of processive degradation of hyaluronan; J. Biol. Chem. 277: 36678-36688 (2002). [pdf]
  138. Mark J. Jedrzejas, Luciane V. Mello, Bert L. de Groot, and Songlin Li; Mechanism of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase: Structures of complexes with the substrate; J. Biol. Chem. 277:28287-28297 (2002). [pdf]
  139. Yoshinori Fujiyoshi, Kaoru Mitsuoka, Bert L. de Groot, Ansgar Philippsen, Helmut Grubmüller, Peter Agre, and Andreas Engel; Structure and function of water channels.; Curr. Opin. Struct. Biol. 12:509-515 (2002). [pdf]
  140. Bert L. de Groot, D. Peter Tieleman, Peter Pohl and Helmut Grubmüller; Water permeation through gramicidin A: desformylation and the double helix; a molecular dynamics study; Biophys. J. 82: 2934-2942 (2002). [pdf]


  141. Bert L. de Groot and Helmut Grubmüller; Water Permeation Across Biological Membranes: Mechanism and Dynamics of Aquaporin-1 and GlpF; Science 294:2353-2357 (2001) [pdf]
  142. Bert L. de Groot, Andreas Engel and Helmut Grubmüller; A refined structure of human aquaporin-1; FEBS Lett. 504:206-211 (2001) [pdf]
  143. Bert L. de Groot, Xavier Daura, Alan E. Mark and Helmut Grubmüller; Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds; J. Mol. Biol. 390 (1): 299-313 (2001) [pdf]


  144. Stahlberg H, Braun T, de Groot B, Philippsen A, Borgnia MJ, Agre P, Kuhlbrandt W, Engel A; The 6.9-angstrom structure of GlpF: A basis for homology modeling of the glycerol channel from Escherichia coli; J. Struct. Biol. 132 (2): 133-141 (2000) [pdf]
  145. Rainer Ossig, Hans Dieter Schmitt, Bert de Groot, Dietmar Riedel, Sirkka Keränen, Hans Ronne, Helmut Grubmüller, and Reinhard Jahn; Exocytosis requires asymmetry in the central layer of the snare complex.; EMBO J. 19:6000-6010 (2000) [pdf]
  146. Bert L. de Groot, J. Bernard Heymann, Andreas Engel, Kaoru Mitsuoka, Yoshinori Fujiyoshi and Helmut Grubmüller; The Fold of Human Aquaporin 1; J. Mol. Biol. 300(4): 987-994 (2000) [pdf]
  147. Heymann J.B, Pfeiffer M, Hildebrandt V, Kaback HR, Fotiadis D, de Groot B, Engel A, Oesterhelt D and Müller D.J.; Conformations of the rhodopsin third cytoplasmic loop grafted onto bacteriorhodopsin; Struct. Fold. Des. 8(6): 643-653 (2000) [pdf]


  148. A.Amadei, B.L. de Groot, M.-A. Ceruso, A. Di Nola and H.J.C. Berendsen; A kinetic model for the internal motions of proteins: Diffusion between multiple harmonic wells , PROTEINS: Struct. Funct. Gen. 35: 283-292 (1999). [pdf]
  149. Bert de Groot; Native state protein dynamics , PhD Thesis, University of Groningen (1999). [pdf]
  150. B.L. de Groot, G. Vriend and H.J.C. Berendsen; Conformational changes in the chaperonin GroEL: New insights into the allosteric mechanism , J. Mol. Biol. 286: 1241-1249 (1999). [pdf]


  151. Johannes P.M. Langedijk, Bert L. de Groot, Herman J.C. Berendsen and Jan T. van Oirschot; Structural homology of the central conserved region of the attachment protein G of the respiratory syncytial virus with the fourth subdomain of 55 kD tumor necrosis factor receptor, Virology 243: 293-302 (1998). [pdf]
  152. B.L. de Groot, S. Hayward, D.M.F. van Aalten, A. Amadei and H.J.C. Berendsen; Domain Motions in Bacteriophage T4 Lysozyme; a Comparison between Molecular Dynamics and Crystallographic Data PROTEINS: Struct. Funct. Gen. 31: 116-127 (1998). [pdf]


  153. B.L. de Groot, D.M.F. van Aalten, R.M. Scheek, A. Amadei, G. Vriend and H.J.C. Berendsen; Prediction of protein conformational freedom from distance constraints, PROTEINS: Struct. Funct. Gen. 29: 240-251 (1997) [pdf]
  154. D.M.F. van Aalten, D.A. Conn, B.L. de Groot, J.B.C. Findlay, H.J.C. Berendsen and A. Amadei; Protein dynamics derived from clusters of crystal structures, Biophys. J. 73(6): 2891-2896 (1997)
  155. D.M.F. van Aalten, B.L. de Groot, H.J.C. Berendsen, J.B.C. Findlay and A. Amadei; A Comparison of Techniques for Calculating Protein Essential Dynamics, J. Comp. Chem. 18:169-181 (1997) [pdf]


  156. D.M.F. van Aalten, B.L. de Groot, H.J.C. Berendsen and J.B.C. Findlay; Conformational analysis of retinoids and restriction of their dynamics by retinoid-binding proteins, Biochemical J. 319(2): 543-550 (1996) [pdf]
  157. D. van der Spoel, B.L. de Groot, S. Hayward, H.J.C. Berendsen and H.J. Vogel; Bending of the Calmodulin Central Helix: A Theoretical Study , Protein Sci. 5: 2044-2053 (1996) [pdf].
  158. B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; An extended sampling of the configurational space of HPr from E. coli , PROTEINS: Struct. Funct. Gen. 26: 314-322 (1996) [pdf].
  159. B.L. de Groot, D.M.F. van Aalten, A. Amadei and H.J.C. Berendsen; The consistency of large concerted motions in proteins in Molecular Dynamics simulations , Biophys. J. 71: 1707-1713 (1996) [pdf]
  160. N.A.J. van Nuland, J.A. Wiersma, D. van der Spoel, B.L. de Groot, R.M. Scheek and G.T. Robillard; Phosphorylation-induced torsion-angle strain in the active center of HPr, detected by NMR and restrained molecular dynamics refinement, Protein Sci. 5: 442-446 (1996)
  161. B.L. de Groot, A. Amadei, D.M.F. van Aalten and H.J.C. Berendsen; Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin, J. Biomol. Struct. Dyn. 13 : 741-751 (1996) [pdf].
  162. A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F. van Aalten and H.J.C. Berendsen; An efficient method for sampling the essential subspace of proteins., J. Biomol. Struct. Dyn. 13:615-626 (1996) [pdf].


  163. R.M. Scheek, N.A.J. van Nuland, B.L. de Groot and A. Amadei; Structure from NMR and molecular dynamics: distance restraining inhibits motion in the essential subspace, J. Biomol. NMR. 6:106-11 (1995) [pdf].
  164. A. Amadei, A.B.M. Linssen, B.L. de Groot and H.J.C. Berendsen; Essential degrees of freedom of proteins, in "Modelling of Biomolecular Structures and Mechanisms" A. Pullmann et. al. (ed.) pp 85-93 (1995) [pdf].

Please note: this webpage is part of the personal CV of Bert de Groot.