2024

  1. Vytautas Gapsys, Wojciech Kopec, Dirk Matthes and Bert L. de Groot. Biomolecular simulations at the exascale: From drug design to organelles and beyond. Curr. Opin. Struct. Biol. . 88: 102887 (2024). [pdf]
  2. Edward Mendez-Otalvaro, Wojciech Kopec and Bert L. de Groot. Effect of two activators on the gating of a K2P channel. Biophys. J. 123: 1-13 (2024). [pdf]
  3. Po-Lin Chiu, Juan D. Orjuela, Bert L. de Groot, Camilo Aponte Santamaria, Thomas Walz. Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts. ELife 12: RP90851 (2024). [pdf]
  4. A. Mironenko, B.L. de Groot and W. Kopec. Selectivity filter mutations shift ion permeation mechanism in potassium channels. PNAS Nexus 3: 7(2024). [pdf]
  5. D.F. Hahn, V. Gapsys, B. L. de Groot, D.L. Mobley, G. Tresadern. rrent State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions. J. Chem. Inf. Model. 64: 5063-5076 (2024). [pdf]
  6. Peng Huang, Hannah Abacka, Carter J. Wilson, Malene Lykke Wind, Michael Rützler, Anna Hagström-Andersson, Pontus Gourdon, Bert L. de Groot, Raminta Venskutonytë, Karin Lindkvist-Petersson. Molecular basis for human aquaporin inhibition. Proc. Nat. Acad. Sci. 121 e2319682121 (2024). [pdf]
  7. Carter J. Wilson, Bert L. de Groot, Vytautas Gapsys. Resolving coupled pH titrations using alchemical free energy calculations. J. Comput. Chem. in press (2023). [pdf]
  8. Drazen Petrov, Jan Walther Perthold, Chris Oostenbrink, Bert L. de Groot, Vytautas Gapsys. Guidelines for Free-Energy Calculations Involving Charge Changes. J. Chem. Theory. Comput. 20:914-925 (2024). [pdf]

    2023

  9. Carter J. Wilson, Mikko Karttunen, Bert L. de Groot, Vytautas Gapsys. Accurately Predicting Protein pKa Values Using Nonequilibrium Alchemy. J. Chem. Theory. Comput. 19:7833-7845 (2023). [pdf]
  10. W. Kopec, A.S. Thomson, B.L. de Groot, B.S. Rothberg. Interactions between selectivity filter and pore helix control filter gating in the MthK channel. J. Gen. Physiol. 155: e202213166 (2023). [pdf]
  11. Chun Kei Lam and Bert L de Groot. Ion Conduction Mechanisms in Potassium Channels Revealed by Permeation Cycles. J. Chem. Theory. Comput. 19:2574-2589 (2023). [pdf]
  12. J. Harry Moore, Christian Margreitter, Jon Paul Janet, Ola Engkvist, Bert L. de Groot, Vytautas Gapsys. Automated relative binding free energy calculations from SMILES to ΔΔG. Comms. Chem. 6: 82 (2023). [pdf]
  13. Ruo-Xu Gu and Bert L. de Groot. Central cavity dehydration as a gating mechanism of potassium channels. Nature Comm. 14: 2178 (2023). [pdf]
  14. Dirk Matthes and Bert .L. de Groot. Molecular dynamics simulations reveal the importance of amyloid-beta oligomer β-sheet edge conformations in membrane permeabilization. J. Biol. Chem. 299: 103034 (2023). [pdf]
  15. Milosz Wieczor, Vito Genna, Juan Aranda, Rosa M. Badia, Josep Lluis Gelpi, Vytautas Gapsys, Bert L. de Groot, Erik Lindahl,Marti Municoy, Adam Hospital, Modesto Orozco. Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case. WIREs computational molecular science. e1622 (2023). [pdf]

    2022

  16. Benedikt Frieg, Leif Antonschmidt, Christian Dienemann, James A Geraets, Eszter E. Najbauer, Dirk Matthes, Bert L. de Groot, Loren B. Andreas, Stefan Becker, Christian Griesinger, Gunnar F. Schröder. The 3D structure of lipidic fibrils of α-synuclein. Nature Comm. 13: 6810 (2022). [pdf]
  17. Leif Antonschmidt, Dirk Matthes, Riza Dervisoglu, Benedikt Frieg, Christian Dienemann, Andrei Leonov, Evgeny Nimerovsky, Vrinda Sant, Sergey Ryazanov, Armin Giese, Gunnar F. Schröder, Stefan Becker, Bert L. de Groot, Christian Griesinger, Loren B. Andreas. The clinical drug candidate anle138b binds in a cavity of lipidic α-synuclein fibrils. Nature Comm. 13: 5385 (2022). [pdf]
  18. Yuriy Khalak, Gary Tresadern, David F. Hahn, Bert L. de Groot, and Vytautas Gapsys. Chemical Space Exploration with Active Learning and Alchemical Free Energies. J. Chem. Theory. Comput. in press (2022). [pdf]
  19. Kalyan S. Chakrabarti, Simon Olsson, Supriya Pratihar, Karin Giller, Kerstin Overkamp, Ko On Lee, Vytautas Gapsys, Kyoung-Seok Ryu, Bert L. de Groot, Frank Noe, Stefan Becker, Donghan Lee, Thomas R. Weikl, Christian Griesinger. A litmus test for classifying recognition mechanisms of transiently binding proteins. Nature Comm. 13: 3792 (2022). [pdf]
  20. Carsten Kutzner, Christian Kniep, Austin Cherian, Ludvig Nordstrom, Helmut Grubmüller, Bert L. de Groot, and Vytautas Gapsys. GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design. J. Chem. Inf. Model. 62: 1691-1711 (2022). [pdf]
  21. Carl Öster, Kumar Tekwani Movellan, Benjamin Goold, Kitty Hendriks, Sascha Lange, Stefan Becker, Bert L. de Groot, Wojciech Kopec, Loren B. Andreas, Adam Lange. Direct Detection of Bound Ammonium Ions in the Selectivity Filter of Ion Channels by Solid-State NMR. J. Am. Chem. Soc. 144: 4147-4157 (2022). [pdf]
  22. V. Gapsys, D.F. Hahn, G. Tresadern, D.L. Mobley, M. Rampp, B.L. de Groot. Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design. J. Chem. Inf. Model. 62: 1172-1177 (2022). [pdf]
  23. Myeongkyu Kim, Jung-Hye Ha, Joonhyeok Choi, Bo-Ram Kim, Vytautas Gapsys, Ko On Lee, Jun-Goo Jee, Kalyan S. Chakrabarti, Bert L. de Groot, Christian Griesinger, Kyoung-Seok Ryu, Donghan Lee. Repositioning Food and Drug Administration-Approved Drugs for Inhibiting Biliverdin IXβ Reductase B as a Novel Thrombocytopenia Therapeutic Target. J. Med. Chem. 65: 2548-2557 (2022). [pdf]

    2021

  24. Yuriy Khalak, Gary Tresadern, Matteo Aldeghi, Hannah Magdalena Baumann, David L. Mobley, Bert L. de Groot, Vytautas Gapsys. Alchemical absolute protein-ligand binding free energies for drug design Chemical Science 12: 13958-13971 (2021). [pdf]
  25. Vytautas Gapsys, Ahmet Yildirim, Matteo Aldeghi, Yuriy Khalak, David van der Spoel, Bert L. de Groot. Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches. Communications Chemistry 4:1-13 (2021). [pdf]
  26. Hannah M. Baumann, Vytautas Gapsys, Bert L. de Groot, and David L. Mobley. Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations. J. Phys. Chem. B 125: 4241-4261 (2021). [pdf]
  27. Raktim N Roy, Kitty Hendriks, Wojciech Kopec, Saeid Abdolvand, Kevin L. Weiss, Bert L. de Groot, Adam Lange, Han Sun, Leighton Coates. Structural plasticity of the selectivity filter in a nonselective ion channel. IUCrJ 8: 421-430 (2021). [pdf]
  28. Eszter E Najbauer, Stefan Becker, Karin Giller, Markus Zweckstetter, Adam Lange, Claudia Steinem, Bert L. de Groot, Christian Griesinger, Loren B. Andreas. Structure, gating and interactions of the voltage-dependent anion channel. Eur. Biophys. J. 50: 159-172 (2021). [pdf]
  29. Martin Werner, Vytautas Gapsys, Bert L. de Groot. One Plus One Makes Three: Triangular Coupling of Correlated Amino Acid Mutations. J. Phys. Chem. Lett. 12: 3195-3201 (2021). [pdf]
  30. Andrei Mironenko, Ulrich Zachariae, Bert L. de Groot, Wojciech Kopec. The persistent question of potassium channel permeation mechanisms. J. Mol. Biol. 433: 167002 (2021). [pdf]
  31. Floris P. Buelens, Hadas Leonov, Bert L. de Groot, and Helmut Grubmüller. ATP-Magnesium Coordination: Protein Structure-Based Force Field Evaluation and Corrections. J. Chem. Theory Comput. 17: 1922-1930 (2021) [pdf]
  32. Yixiao Zhang, Csaba Daday, Ruo-Xu Gu, Charles D. Cox, Boris Martinac, Bert L. de Groot and Thomas Walz. Visualization of the mechanosensitive ion channel MscS under membrane tension. Nature 590: 509-514 (2021). [pdf]
  33. Yuriy Khalak, Gary Tresadern, Bert L. de Groot and Vytautas Gapsys. Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software. J. Comput. Aided Mol. Des. 35: 49-61 (2021). [pdf]
  34. Csaba Daday and Bert L. de Groot. Lipid-protein forces predict conformational changes in a mechanosensitive channel. Eur. Biophys. J. 50: 181-186 (2021). [pdf]

    2020

  35. Fabian Rabe von Pappenheim, Matteo Aldeghi, Brateen Shome, Tadhg Begley, Bert L. de Groot, Kai Tittmann. Structural basis for antibiotic action of the B 1 antivitamin 2'-methoxy-thiamine. Nature Chem. Biol. 16:1237-1245 (2020). [pdf]
  36. Tobias Schubeis, Tanguy Le Marchand, Csaba Daday, Wojciech Kopec, Kumar Tekwani Movellan, Jan Stanek, Tom S. Schwarzer, Kathrin Castiglione, Bert L. de Groot, Guido Pintacuda, Loren B. Andreas. A β-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkL. Proc. Nat. Acad. Sci. 117: 21014-21021 (2020). [pdf]
  37. Vytautas Gapsys, Bert L. de Groot. On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size. eLife. 9: e57589 (2020). [pdf]
  38. Vytautas Gapsys, Morteza Khabiri, Bert L. de Groot, and Peter L. Freddolino. Comment on "Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes" J. Phys. Chem. B. 124: 1115-1123 (2020). [pdf]
  39. Patricia S. Langan, Venu Gopal Vandavasi, Wojciech Kopec, Brendan Sullivan, Pavel V. Afonne, Kevin L. Weiss, Bert L. de Groot, Leighton Coates. The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation. IUCrJ. 7: 1-9 (2020). [pdf]
  40. Tomas Bastys, Vytautas Gapsys, Hauke Walter, Eva Heger, Nadezhda T. Doncheva, Rolf Kaiser, Bert L. de Groot, Olga V. Kalinina. Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors. Retrovirology. 17: 1-14 (2020). [pdf]
  41. Ruo-Xu Gu, Bert L. de Groot. Lipid-protein interactions modulate the conformational equilibrium of a potassium channel. Nature Communications. 11: 1-10 (2020). [pdf]
  42. Sofia W de Mare, Raminta Venskutonyte, Sandra Eltschkner, Bert L. de Groot, Karin Lindkvist-Petersson. Structural Basis for Glycerol Efflux and Selectivity of Human Aquaporin 7. Structure. 28: 215-222.e3 (2020). [pdf]
  43. Andrea Rizzi, Travis Jensen, David R. Slochower, Matteo Aldeghi, Vytautas Gapsys, Dimitris Ntekoumes, Stefano Bosisio, Michail Papadourakis, Niel M. Henriksen, Bert L. De Groot, Zoe Cournia, Alex Dickson, Julien Michel, Michael K. Gilson, Michael R. Shirts, David L. Mobley, John D. Chodera. The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations. J. Comput. Aided Mol. Des. 34: 601-633 (2020). [pdf]
  44. Colin A Smith, Adam Mazur, Ashok K Rout, Stefan Becker, Donghan Lee, Bert L de Groot, Christian Griesinger. Enhancing NMR derived ensembles with kinetics on multiple timescales. Journal of Biomolecular NMR. 74: 27-43 (2020). [pdf]
  45. Vytautas Gapsys, Laura Perez-Benito, Matteo Aldeghi, Daniel Seeliger, Herman van Vlijmen, Gary Tresadern, Bert L de Groot. Large scale relative protein ligand binding affinities using non-equilibrium alchemy. Chemical Science. 11: 1140-1152 (2020). [pdf]

    2019

  46. Wojciech Kopec, Brad S. Rothberg, Bert L. de Groot. Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling. Nature Communications. 10: 5366 (2019). [pdf]
  47. Eddy Elisée, Vytautas Gapsys, Nawel Mele, Ludovic Chaput, Edithe Selwa, Bert L de Groot, Bogdan I Iorga. Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset. J. Comput. Aided Mol. Des. 1573-4951 (2019). [pdf]
  48. Matteo Aldeghi, Vytautas Gapsys and Bert L. de Groot. Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches. ACS Cent. Sci. 5:1468-1474 (2019). [pdf]
  49. Carsten Kutzner, Szilard Pall, Martin Fechner, Ansgar Esztermann Bert L. de Groot, Helmut Grubmüller. More bang for your buck: Improved use of GPU nodes for GROMACS 2018. J. Comp. Chem. J. 40: 2418-2431 (2019). [pdf]
  50. Carl Öster, Kitty Hendriks, Wojciech Kopec, Veniamin Chevelkov, Chaowei Shi, Dagmar Michl, Sascha Lange, Han Sun, Bert L. de Groot, Adam Lange. The conduction pathway of potassium channels is water free under physiological conditions. Science Advances 5: eaaw6756 (2019). [pdf]
  51. Vytautas Gapsys and Bert L. de Groot. Comment on'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'. eLife 8:e44718 (2019). [pdf]
  52. Fabian Paul, Hao Wu, Maximilian Vossel, Bert L de Groot, Frank Noé. Identification of kinetic order parameters for non-equilibrium dynamics. J. Chem. Phys. 16:164120 (2019). [pdf]
  53. Chen Song, Bert L. de Groot, Mark S.P. Sansom. Lipid Bilayer Composition Influences the Activity of the Antimicrobial Peptide Dermcidin Channel. Biophys. J. 116: 1658-1666 (2019). [pdf]
  54. Emanuele G. Coci, Vytautas Gapsys, Natasha Shur , Yoon Shin-Podskarbi, Bert L. de Groot, Kathryn Miller, Jerry Vockley, Neal Sondheimer, Rebecca Ganetzky, Peter Freisinger. Pyruvate carboxylase deficiency type A and type C: Characterization of five novel pathogenic variants in PC and analysis of the genotype-phenotype correlation. Human mutation 1-12 (2019). [pdf]
  55. Ai Woon Yee, Matteo Aldeghi, Matthew P. Blakeley, Andreas Ostermann, Philippe J. Mas, Martine Moulin, Daniele de Sanctis, Matthew W. Bowler, Christoph Mueller-Dieckmann, Edward P Mitchell, Michael Haertlein, Bert L. de Groot, Elisabetta Boeri Erba, V. Trevor Forsyth. A molecular mechanism for transthyretin amyloidogenesis. Nature communications 10: 925 (2019). [pdf]
  56. Marcus Schewe, Han Sun, Ümit Mert, Alexandra Mackenzie, Ashley CW Pike, Friederike Schulz, Cristina Constantin, Kirsty S. Vowinkel, Linus J. Conrad, Aytug K. Kiper, Wendy Gonzalez, Marianne Musinszki, Marie Tegtmeier, David C. Pryde, Hassane Belabed, Marc Nazare, Bert L. de Groot, Niels Decher, Bernd Fakler, Elisabeth P. Carpenter, Stephen J. Tucker, Thomas Baukrowitz. A pharmacological master key mechanism that unlocks the selectivity filter gate in K+ channels. Science 363: 875-880 (2019). [pdf]
  57. 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. 116: 1059-1061 (2019). [pdf]
  58. 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. 141: 858-869 (2019). [pdf]
  59. 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]
  60. 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]
  61. 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]

    2018

  62. 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]
  63. Julian T Brennecke, Bert L de Groot. Quantifying Asymmetry of Multimeric Proteins. J. Phys. Chem. A 122:7924-7930 (2018). [pdf]
  64. 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]
  65. 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. 14: 3397−3408 (2018). [pdf]
  66. 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]
  67. 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]
  68. 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]
  69. 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]

    2017

  70. 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]
  71. 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]
  72. 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]
  73. 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]
  74. 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]
  75. 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]
  76. Vytautas Gapsys, Bert L de Groot. pmx Webserver: A User Friendly Interface for Alchemistry. J. Chem. Inf. Model. 57: 109-114 (2017). [pdf]
  77. 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]
  78. 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]
  79. 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]

    2016

  80. 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]
  81. 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]
  82. 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]
  83. 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]
  84. 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]
  85. 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]
  86. Marco Singer Tatyana Krivobokova, Axel Munk, and Bert L. de Groot. Partial least squares for dependent data. Biometrika 103 351-362 (2016) [pdf]
  87. 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]
  88. 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]
  89. 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]

    2015

  90. 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]
  91. 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]
  92. 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]
  93. 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]
  94. 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]
  95. 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]
  96. 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]
  97. 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]
  98. 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]
  99. 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]

    2014

  100. 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]
  101. 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]
  102. 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]
  103. 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]

    2013

  104. 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]
  105. 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]
  106. Vytautas Gapsys, Bert L. de Groot, Rodolfo Briones. Computational analysis of local membrane properties. J. Comput. Aided Mol. Des. 27: 845-858 (2013). [pdf]
  107. Martin Vesper and Bert L. de Groot. Collective Dynamics Underlying Allosteric Transitions in Hemoglobin. PLoS Comp. Biol. 9: e1003232 (2013). [pdf]
  108. 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]
  109. 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]
  110. 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]
  111. 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]
  112. Vytautas Gapsys and Bert L. de Groot. Optimal superpositioning of flexible molecule ensembles. Biophys. J. 104:196-207 (2013). [pdf] [supplement pdf]
  113. 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]

    2012

  114. 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]
  115. 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]
  116. 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]
  117. 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]
  118. 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]
  119. 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]
  120. 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]
  121. 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]
  122. 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]
  123. 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]

    2011

  124. 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]
  125. 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]
  126. 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]
  127. 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]
  128. 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]
  129. 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]
  130. 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]
  131. 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]

    2010

  132. 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]
  133. 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]
  134. 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]
  135. 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]
  136. 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]
  137. 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]
  138. 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]
  139. Daniel Seeliger and Bert L. de Groot. Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J. Comput. Aided Mol. Des. 24:417-422 (2010). [pdf]
  140. 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]
  141. Daniel Seeliger and Bert L. de Groot. Protein thermostability calculations using alchemical free energy simulations. Biophys. J. 98:2309-2316 (2010). [pdf] [supplement pdf]
  142. 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]
  143. 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]
  144. 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]
  145. 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]

    2009

  146. Jochen S. Hub and Bert L. de Groot. Detection of functional modes in protein dynamics. PLOS Comput. Biol. 5: e1000480 (2009).[pdf]
  147. 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]
  148. 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]
  149. 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]
  150. 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]
  151. 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]
  152. 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]
  153. 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]
  154. 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]
  155. Daniel Seeliger and Bert L. de Groot. tCONCOORD-GUI: Visually Supported Conformational Sampling of Bioactive Molecules. J. Comp. Chem. 30:1160-1166 (2009). [pdf]

    2008

  156. 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]
  157. 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]
  158. 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]
  159. 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]
  160. 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]
  161. 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]
  162. 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]
  163. 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]
  164. Jochen S. Hub and Bert L. de Groot. Mechanism of selectivity in aquaporins and aquaglyceroporins Proc. Nat. Acad. Sci. 105:1198-1203 (2008).[pdf]
  165. 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]

    2007

  166. Daniel Seeliger, Jürgen Haas, and Bert L. de Groot. Geometry-based Sampling of Conformational Transitions in Proteins. Structure 15: 1482-1492 (2007).[pdf]
  167. 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]
  168. 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]
  169. 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]
  170. 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]
  171. 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]
  172. 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]

    2006

  173. 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]
  174. 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]
  175. 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]
  176. Jochen S. Hub and Bert L. de Groot. Does CO2 Permeate through Aquaporin-1? Biophys. J. 91:842-848 (2006). [pdf]
  177. 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]
  178. Daniel Seeliger and Bert L. de Groot. Prediction of protein flexibility from geometrical constraints. Biotech International. 18:20-22 (2006). [pdf]
  179. 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]
  180. 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]
  181. J. B. Sörensen, 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]
  182. 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]

    2005

  183. 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]
  184. 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]
  185. 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]
  186. 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]
  187. 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]
  188. 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]

    2004

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

    2003

  190. 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]
  191. 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]

    2002

  192. 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]
  193. 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]
  194. 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]
  195. 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]
  196. 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]

    2001

  197. 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]
  198. Bert L. de Groot, Andreas Engel and Helmut Grubmüller; A refined structure of human aquaporin-1; FEBS Lett. 504:206-211 (2001) [pdf]
  199. 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]

    2000

  200. 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]
  201. 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]
  202. 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]
  203. 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]

    1999

  204. 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]
  205. Bert de Groot; Native state protein dynamics , PhD Thesis, University of Groningen (1999). [pdf]
  206. 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]

    1998

  207. 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]
  208. 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]

    1997

  209. 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]
  210. 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)
  211. 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]

    1996

  212. 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]
  213. 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].
  214. 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].
  215. 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]
  216. 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)
  217. 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].
  218. 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].

    1995

  219. 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].
  220. 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.