Journal Article (145)

  1. Journal Article
    Kutzner, C.; Páll, S.; Fechner, M.; Esztermann, A.; de Groot, B. L.; Grubmüller, H.: More bang for your buck: Improved use of GPU nodes for GROMACS 2018. Journal of Computational Chemistry 40 (27), pp. 2418 - 2431 (2019)
  2. Journal Article
    Öster, C.; Hendriks, K.; Kopec, W.; Chevelkov, V.; Shi, C.; Michl, D.; Lange, S.; Sun, H.; de Groot, B. L.; Lange, A.: The conduction pathway of potassium channels is water free under physiological conditions. Science Advances 5 (7) (2019)
  3. Journal Article
    Gapsys, V.; de Groot, B. L.: Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'. eLife 8 (2019)
  4. Journal Article
    Coci, E. G.; Gapsys, V.; Shur, N.; Shin‐Podskarbi, Y.; de Groot, B.; Miller, K.; Vockley, J.; Sondheimer, N.; Ganetzky, R.; Freisinger, P.: Pyruvate carboxylase deficiency type A and type C: Characterization of 5 novel pathogenic variants in PC and analysis of the genotype-phenotype correlation. Human Mutation 40 (6), pp. 816 - 827 (2019)
  5. Journal Article
    Song, C.; de Groot, B. L.; Sansom, M. S. P.: Lipid bilayer composition influences the activity of the antimicrobial peptide dermcidin channel. Biophysical Journal 116 (9), pp. 1658 - 1666 (2019)
  6. Journal Article
    Heifetz, A.; James, T.; Southey, M.; Morao, I.; Aldeghi, M.; Sarrat, L.; Fedorov, D. G.; Bodkin, M. J.; Townsend-Nicholson, A.: Characterising GPCR-ligand interactions using a fragment molecular orbital-based approach. Current Opinion in Structural Biology 55, pp. 85 - 92 (2019)
  7. Journal Article
    Yee, A. W.; Aldeghi, M.; Blakeley, M. P.; Ostermann, A.; Mas, P. J.; Moulin, M.; de Sanctis, D.; Bowler, M. W.; Mueller-Dieckmann, C.; Mitchell, E. P. et al.; Haertlein, M.; de Groot, B. L.; Boeri Erba, E.; Forsyth, V. T.: A molecular mechanism for transthyretin amyloidogenesis. Nature Communications 10 (1) (2019)
  8. Journal Article
    Schewe, M.; Sun, H.; Mert, Ü.; Mackenzie, A.; Pike, A. C. W.; Schulz, F.; Constantin, C.; Vowinkel, K. S.; Conrad, L. J.; Kiper, A. K. et al.; Gonzalez, W.; Musinszki, M.; Tegtmeier, M.; Pryde, D. C.; Belabed, H.; Nazare, M.; de Groot, B. L.; Decher, N.; Fakler, B.; Carpenter, E. P.; Tucker, S. J.; Baukrowitz, T.: A pharmacological master key mechanism that unlocks the selectivity filter gate in K+ channels. Science 363 (6429), pp. 875 - 880 (2019)
  9. Journal Article
    Awasthi, N.; Kopec, W.; Wilkosz, N.; Jamroz, D.; Hub, J. S.; Zatorska, M.; Petka, R.; Nowakowska, M.; Kepczynski, M.: Molecular mechanism of polycation-induced pore formation in biomembranes. ACS Biomaterials Science and Engineering 5 (2), pp. 780 - 794 (2019)
  10. Journal Article
    Cordeiro, S.; Finol-Urdaneta, R. K.; Köpfer, D.; Markushina, A.; Song, J.; French, R. J.; Kopec, W.; de Groot, B. L.; Giacobassi, M. J.; Leavitt, L. S. et al.; Raghuraman, S.; Teichert, R. W.; Olivera, B. M.; Terlau, H.: Conotoxin κM-RIIIJ, a tool targeting asymmetric heteromeric Kv1 channels. Proceedings of the National Academy of Sciences of the United States of America 116 (3), pp. 1059 - 1064 (2019)
  11. Journal Article
    Briones, R.; Blau, C.; Kutzner, C.; de Groot, B. L.; Aponte-Santamaría, C.: GROmaρs: A GROMACS-based toolset to analyze density maps derived from molecular dynamics simulations. Biophysical Journal 116 (1), pp. 4 - 11 (2019)
  12. Journal Article
    Lutz, H.; Jaeger, V.; Weidner, T.; de Groot, B. L.: Interpretation of interfacial protein spectra with enhanced molecular simulation ensembles. Journal of Chemical Theory and Computation 15 (1), pp. 698 - 707 (2019)
  13. Journal Article
    Aldeghi, M.; Gapsys, V.; de Groot, B. L.: Predicting kinase inhibitor resistance: Physics-based and data-driven approaches. ACS Central Science 5 (8), pp. 1468 - 1474 (2019)
  14. Journal Article
    Gu, R. X.; Baoukina, S.; Tieleman, D. P.: Cholesterol flip-flop in heterogeneous membranes. Journal of Chemical Theory and Computation 15 (3), pp. 2064 - 2070 (2019)
  15. Journal Article
    Paul, F.; Wu, H.; Vossel, M.; de Groot, B. L.; Noé, F.: Identification of kinetic order parameters for non-equilibrium dynamics. The Journal of Chemical Physics 150 (16), 164120 (2019)
  16. Journal Article
    Rovo, P.; Smith, C. A.; Gauto, D.; de Groot, B. L.; Schanda, P.; Linser, R.: Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society 141 (2), pp. 858 - 869 (2019)
  17. Journal Article
    Aldeghi, M.; Gapsys, V.; de Groot, B. L.: Accurate estimation of ligand binding affinity changes upon protein mutation. ACS Central Science 4 (12), pp. 1708 - 1718 (2018)
  18. Journal Article
    Brennecke, J. T.; de Groot, B. L.: Quantifying asymmetry of multimeric proteins. The Journal of Physical Chemistry A 122 (39), pp. 7924 - 7930 (2018)
  19. Journal Article
    Kopec, W.; Köpfer, D.; Vickery, O. N.; Bondarenko, A. S.; Jansen, T. L. C.; de Groot, B. L.; Zachariae, U.: Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels. Nature Chemistry 10 (8), pp. 813 - 820 (2018)
  20. Journal Article
    Bastys, T.; Gapsys, V.; Doncheva, N. T.; Kaiser, R.; de Groot, B. L.; Kalinina, O. V.: Consistent prediction of mutation effect on drug binding in HIV-1 protease using alchemical calculations. Journal of Chemical Theory and Computation 14 (7), pp. 3397 - 3408 (2018)
  21. Journal Article
    Heinz, L. P.; Kopec, W.; de Groot, B. L.; Fink, R. H. A.: In silico assessment of the conduction mechanism of the ryanodine receptor 1 reveals previously unknown exit pathways. Scientific Reports 8 (2018)
  22. Journal Article
    Sabo, T. M.; Gapsys, V.; Walter, K. F. A.; Fenwick, R. B.; Becker, S.; Salvatella, X.; de Groot, B. L.; Lee, D.; Griesinger, C.: Utilizing dipole-dipole cross-correlated relaxation for the measurement of angles between pairs of opposing CαHα-CαHα bonds in anti-parallel β-sheets. Methods 138-139, pp. 85 - 92 (2018)
  23. Journal Article
    Brennecke, J. T.; de Groot, B. L.: Mechanism of mechanosensitive gating of the TREK-2 potassium channel. Biophysical Journal 114 (6), pp. 1336 - 1343 (2018)
  24. Journal Article
    Shi, C.; He, Y.; Hendriks, K.; de Groot, B. L.; Cai, X.; Tian, C.; Lange, A.; Sun, H.: A single NaK channel conformation is not enough for non-selective ion conduction. Nature Communications 9 (2018)
  25. Journal Article
    Matthes, D.; Gapsys, V.; Griesinger, C.; de Groot, B. L.: Resolving the atomistic modes of anle138b inhibitory action on peptide oligomer formation. ACS Chemical Neuroscience 8 (12), pp. 2791 - 2808 (2017)
  26. Journal Article
    Gapsys, V.; de Groot, B. L.: Alchemical free energy calculations for nucleotide mutations in protein-DNA complexes. Journal of Chemical Theory and Computation 13 (12), pp. 6275 - 6289 (2017)
  27. Journal Article
    Ban, D.; Smith, C. A.; de Groot, B. L.; Griesinger, C.; Lee, D.: Recent advances in measuring the kinetics of biomolecules by NMR relaxation dispersion spectroscopy. Archives of Biochemistry and Biophysics 628, pp. 81 - 91 (2017)
  28. Journal Article
    Aponte-Santamaria, C.; Fischer, G.; Bath, P.; Neutze, R.; de Groot, B. L.: Temperature dependence of protein-water interactions in a gated yeast aquaporin. Scientific Reports 7 (2017)
  29. Journal Article
    Machtens, J. P.; Briones, R.; Alleva, C.; de Groot, B. L.; Fahlke, C.: Gating charge calculations by computational electrophysiology simulations. Biophysical Journal 112 (7), pp. 1396 - 1405 (2017)
  30. Journal Article
    Saboe, P. O.; Rapisarda, C.; Kaptan, S.; Hsiao, Y. S.; Summers, .. R.; De Zorzi, R.; Dukovski, D.; Yu, J.; de Groot, B. L.; Kumar, M. et al.; Walz, T.: Role of pore-lining residues in defining the rate of water conduction by Aquaporin-0. Biophysical Journal 112 (5), pp. 953 - 965 (2017)
  31. Journal Article
    Briones, R.; Aponte-Santamaria, C.; de Groot, B. L.: Localization and ordering of lipids around Aquaporin-0: Proteinand lipid mobility effects. Frontiers in Physiology 8 (2017)
  32. Journal Article
    Gapsys, V.; de Groot, B. L.: pmx Webserver: A user friendly interface for alchemistry. Journal of Chemical Information and Modeling 57 (2), pp. 109 - 114 (2017)
  33. Journal Article
    Huang, J.; Rauscher, S.; Nawrocki, G.; Ran, T.; Feig, M.; de Groot, B. L.; Grubmüller, H.; MacKerell, A. D.: CHARMM36m: An improved force field for folded and intrinsically disordered proteins. Nature Methods 14 (1), pp. 71 - 73 (2017)
  34. Journal Article
    Briones, R.; Weichbrodt, C.; Paltrinieri, L.; Mey, I.; Villinger, S.; Giller, K.; Lange, A.; Zweckstetter, M.; Griesinger, C.; Becker, S. et al.; Steinem, C.; de Groot, B. L.: Voltage dependence of conformational dynamics and subconducting states of VDAC-1. Biophysical Journal 111 (6), pp. 1223 - 1234 (2016)
  35. Journal Article
    Ilgü, H.; Jeckelmann, J. M.; Gapsys, V.; Ucurum, Z.; de Groot, B. L.; Fotiadis, D.: Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC. Proceedings of the National Academy of Sciences of the United States of America 113 (37) (2016)
  36. Journal Article
    Matthes, D.; Gapsys, V.; Brennecke, J. T.; de Groot, B. L.: An atomistic view of amyloidogenic self-assembly: Structure and dynamics of heterogeneous conformational states in the pre-nucleation phase. Scientific Reports 6 (2016)
  37. Journal Article
    Assentoft, M.; Kaptan, S.; Schneider, H. P.; Deitmer, J. W.; de Groot, B. L.; MacAulay, N.: Aquaporin 4 as a NH3 channel. Journal of Biological Chemistry 291 (36), pp. 19184 - 19195 (2016)
  38. Journal Article
    Kutzner, C.; Köpfer, D.; Machtens, J. P.; de Groot, B. L.; Song, C.; Zachariae, U.: Insights into the function of ion channels by computational electrophysiology simulations. Biochimica et Biophysica Acta - Biomembranes 1858 (7, B), pp. 1741 - 1752 (2016)
  39. Journal Article
    Gapsys, V.; Michielssens, S.; Seeliger, D.; de Groot, B. L.: Accurate and rigorous prediction of the changes in protein free energies in a large-scale mutation scan. Angewandte Chemie-International Edition 55 (26), pp. 7364 - 7368 (2016)
  40. Journal Article
    Singer, M.; Krivobokova, T.; Munk, A.; De Groot, B. L.: Partial least squares for dependent data. Biometrika 103 (2), pp. 351 - 362 (2016)
  41. Journal Article
    Kirscht, A.; Kaptan, S. S.; Bienert, G. P.; Chaumont, F.; Nissen, P.; de Groot, B. L.; Kjellbom, P.; Gourdon, P.; Johanson, U.: Crystal structure of an ammonia-permeable aquaporin. PLOS Biology 14 (3) (2016)
  42. Journal Article
    Smith, C. A.; Ban, D.; Pratihar, S.; Giller, K.; Paulat, M.; Becker, S.; Griesinger, C.; Lee, D.; de Groot, B. L.: Allosteric switch regulates protein–protein binding through collective motion. Proceedings of the National Academy of Sciences of the United States of America 113 (12) (2016)
  43. Journal Article
    Schewe, M.; Nematian-Ardestani, E.; Sun, H.; Musinszki, M.; Cordeiro, S.; Bucci, G.; de Groot, B. L.; Tucker, S. J.; Rapedius, M.; Baukrowitz, T.: A non-canonical voltage sensor controls gating in K2P K2 channels. Cell 164 (5), pp. 937 - 949 (2016)
  44. Journal Article
    Kaptan, S.; Assentoft, M.; Schneider, H. P.; Fenton, R. A.; Deitmer, J. W.; MacAulay, N.; de Groot, B. L.: H95 is a pH-dependent gate in Aquaporin 4. Structure 23 (12), pp. 2309 - 2318 (2015)
  45. Journal Article
    Rose, A. S.; Zachariae, U.; Grubmüller, H.; Hofmann, K. P.; Scheerer, P.; Hildebrand, W.: Role of structural dynamics at the receptor G protein interface for signal transduction. PLOS One 10 (11) (2015)
  46. Journal Article
    Rauscher, S.; Gapsys, V.; Gajda, M. J.; Zweckstetter, M.; de Groot, B. L.; Grubmüller, H.: Structural ensembles of intrinsically disordered proteins depend strongly on force field: A comparison to experiment. Journal of Chemical Theory and Computation 11 (11), pp. 5513 - 5524 (2015)
  47. Journal Article
    Gapsys, V.; Narayanan, R. L.; Xiang, S.; de Groot, B. L.; Zweckstetter, M.: Improved validation of IDP ensembles by one-bond Cα-Hα scalar couplings. Journal of Biomolecular NMR 63 (3), pp. 299 - 307 (2015)
  48. Journal Article
    Kutzner, C.; Páll, S.; Fechner, M.; Esztermann, A.; de Groot, B.; Grubmüller, H.: Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. Journal of Computational Chemistry 36 (26), pp. 1990 - 2008 (2015)
  49. Journal Article
    Linser, R.; Salvi, N.; Briones, R.; Rovo, P.; de Groot, B. L.; Wagner, G.: The membrane anchor of the transcriptional activator SREBP is characterized by intrinsic conformational flexibility. Proceedings of the National Academy of Sciences of the United States of America 112 (40) (2015)
  50. Journal Article
    Kutzner, C.; Páll, S.; Fechner, M.; Esztermann, A.; De Groot, B.; Grubmueller, H.: Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. arXiv (2015)
  51. Journal Article
    Andrini, O.; Keck, M.; Briones, R.; Lourdel, S.; Vargas-Poussou, R.; Teulon, J.: ClC-K chloride channels: Emerging pathophysiology of Bartter syndrome type 3. American Journal of Physiology-Renal Physiology 308 (12) (2015)
  52. Journal Article
    Michielssens, S.; de Groot, B. L.; Grubmüller, H.: Binding affinities controlled by shifting conformational equilibria: Opportunities and limitations. Biophysical Journal 108 (10), pp. 2585 - 2590 (2015)
  53. Journal Article
    Gapsys, V.; Michielssens, S.; Seeliger, D.; de Groot, B. L.: Pmx: Automated protein structure and topology generation for alchemical perturbations. Journal of Computational Chemistry 36 (5), pp. 348 - 354 (2015)
  54. Journal Article
    Machtens, J. P.; Kortzak, D.; Lansche, C.; Leinenweber, A.; Kilian, P.; Begemann, B.; Zachariae, U.; Ewers, D.; de Groot, B. L.; Briones, R. et al.; Fahlke, C.: Mechanisms of anion conduction by coupled glutamate transporters. Cell 160 (3), pp. 542 - 553 (2015)
  55. Journal Article
    Smith, C. A.; Ban, D.; Pratihar, S.; Giller, K.; Schwiegk, C.; de Groot, B. L.; Becker, S.; Griesinger, C.; Lee, D.: Population shuffling of protein conformations. Angewandte Chemie International Edition 54 (1), pp. 207 - 210 (2015)
  56. Journal Article
    Köpfer, D.; Song, C.; Gruene, T.; Sheldrick, G. M.; Zachariae, U.; de Groot, B. L.: Ion permeation in K+ channels occurs by direct Coulomb knock-on. Science 345 (6207), pp. 352 - 355 (2014)
  57. Journal Article
    Michielssens, S.; Peters, J. H.; Ban, D.; Pratihar, S.; Seeliger, D.; Sharma, M.; Giller, K.; Sabo, T. M.; Becker, S.; Lee, D. et al.; Griesinger, C.; de Groot, B. L.: A designed conformational shift to control protein binding specificity. Angewandte Chemie International Edition 53 (39), pp. 10367 - 10371 (2014)
  58. Journal Article
    Matthes, D.; Daebel, V.; Meyenberg, K.; Riedel, D.; Heim, G.; Diederichsen, U.; Lange, A.; De Groot, B. L.: Spontaneous aggregation of the insulin-derived steric zipper peptide VEALYL results in different aggregation forms with common features. Journal of Molecular Biology 426 (2), pp. 362 - 376 (2014)
  59. Journal Article
    Hub, J. S.; de Groot, B. L.; Grubmüller, H.; Groenhof, G.: Quantifying artifacts in Ewald simulations of inhomogeneous systems with a net charge. Journal of Chemical Theory and Computation 10 (1), pp. 381 - 390 (2014)
  60. Journal Article
    Xiang, S. Q.; Gapsys, V.; Kim, H. Y.; Bessonov, S.; Hsiao, H. H.; Möhlmann, S.; Klaukien, V.; Ficner, R.; Becker, S.; Urlaub, H. et al.; Lührmann, R.; de Groot, B.; Zweckstetter, M.: Phosphorylation drives a dynamic switch in serine/arginine-rich proteins. Structure 21 (12), pp. 2162 - 2174 (2013)
  61. Journal Article
    Gapsys, V.; de Groot, B. L.; Briones, R.: Computational analysis of local membrane properties. Journal of Computer-Aided Molecular Design 27 (10) (2013)
  62. Journal Article
    Paltrinieri, L.; Borsari, M.; Battistuzzi, G.; Sola, M.; Dennison, C.; de Groot, B. L.; Corni, S.; Bortolotti, C. A.: How the dynamics of the metal-binding loop region controls the acid transition in cupredoxins. Biochemistry 52 (42), pp. 7397 - 7404 (2013)
  63. Journal Article
    Vesper, M. D.; de Groot, B. L.: Collective dynamics underlying allosteric transitions in hemoglobin. PLoS Computational Biology 9 (9) (2013)
  64. Journal Article
    Assentoft, M.; Kaptan, S.; Fenton, R. A.; Hua, S. Z.; de Groot, B. L.; MacAulay, N.: Phosphorylation of rat aquaporin-4 at Ser111 is not required for channel gating. Glia 61 (7), pp. 1101 - 1112 (2013)
  65. Journal Article
    Lindner, T.; de Groot, B. L.; Stary-Weinzinger, A.: Probing the energy landscape of activation gating of the bacterial potassium channel KcsA. PLoS Computational Biology 9 (5) (2013)
  66. Journal Article
    Wacker, S.; Aponte-Santamaria, C. A.; Kjellbom, P.; Nielsen, S.; de Groot, B. L.; Rützler, M.: The identification of novel, high affinity AQP9 inhibitors in an intracellular binding site. Molecular Membrane Biology 30 (3), pp. 246 - 260 (2013)
  67. Journal Article
    Song, C.; Weichbrodt, C.; Salnikov, E.; Dynowski, M.; Forsberg, B.; Bechinger, B.; Steinem, C.; de Groot, B. L.; Zachariae, U.; Zeth, K.: Crystal structure and functional mechanism of a human antimicrobial membrane channel. Proceedings of the National Academy of Sciences of the United States of America 110 (12), pp. 4586 - 4591 (2013)
  68. Journal Article
    Seeliger, D.; Zapater, C.; Krenc, D.; Haddoub, R.; Flitsch, S.; Beitz, E.; Cerdà, J.; De Groot, B. L.: Discovery of novel human aquaporin-1 blockers. ACS Chemical Biology 8 (1), pp. 249 - 256 (2013)
  69. Journal Article
    Gapsys, V.; de Groot, B. L.: Optimal superpositioning of flexible molecule ensemble. Biophysical Journal 104 (1), pp. 196 - 207 (2013)
  70. Journal Article
    Peters, J. H.; de Groot, B. L.: Ubiquitin dynamics in complexes reveal molecular recognition mechanisms beyond induced fit and conformational selection. PLoS Computational Biology 8 (10) (2012)
  71. Journal Article
    Zachariae, U.; Schneider, R.; Briones, R.; Gattin, Z.; Demers, J. P.; Giller, K.; Maier, E.; Zweckstetter, M.; Griesinger, C.; Becker, S. et al.; Benz, R.; de Groot, B. L.; Lange, A.: Beta-barrel mobility underlies closure of the voltage-dependent anion channel. Structure 20 (9), pp. 1540 - 1549 (2012)
  72. Journal Article
    Krivobokova, T.; Briones, R.; Hub, J. S.; Munk, A.; de Groot, B. L.: Partial least squares functional mode analysis: Application to the membrane proteins AQP1, Aqy1 and CLC-ec1. Biophysical Journal 103 (4), pp. 786 - 796 (2012)
  73. Journal Article
    Matthes, D.; Gapsys, V.; de Groot, B. L.: Driving forces and structural determinants of steric zipper peptide oligomer formation elucidated by atomistic simulations. Journal of Molecular Biology 421 (2-3), pp. 390 - 416 (2012)
  74. Journal Article
    Michielssens, S.; van Erp, T. S.; Kutzner, C.; Ceulemans, A.; de Groot, B. L.: Molecular dynamics in principal component space. Journal of Physical Chemistry B 116 (29), pp. 8350 - 8357 (2012)
  75. Journal Article
    Köpfer, D.; Hahn, U.; Ohmert, I.; Vriend, G.; Pongs, O.; de Groot, B. L.; Zachariae, U.: A molecular switch driving inactivation in the cardiac K+ channel hERG. PLoS One 7 (7) (2012)
  76. Journal Article
    Gapsys, V.; Seeliger, D.; de Groot, B. L.: New soft-core potential function for molecular dynamics based alchemical free energy calculations. Journal of Chemical Theory and Computation 8 (7), pp. 2373 - 2382 (2012)
  77. Journal Article
    Aponte-Santamaria, C. A.; Briones, R.; Schenk, A. D.; Walz, T.; de Groot, B. L.: Molecular driving forces defining lipid positions around aquaporin-0. Proceedings of the National Academy of Sciences of the United States of America 109 (25), pp. 9887 - 9892 (2012)
  78. Journal Article
    Portella, G.; Polupanow, T.; Zocher, F.; Boytsov, D. A.; Pohl, P.; Diederichsen, U.; de Groot, B. L.: Design of peptide-membrane interactions to modulate single-file water transport through modified gramicidin channels. Biophysical Journal 103 (8), pp. 1698 - 1705 (2012)
  79. Journal Article
    Wacker, S. J.; Jurkowski, W.; Simmons, K. J.; Fishwick, C. W. G.; Johnson, A. P.; Madge, D.; Lindahl, E.; Rolland, J. F.; de Groot, B. L.: Identification of selective inhibitors of the potassium channel Kv1.1–1.2(3) by high-throughput virtual screening and automated patch clamp. ChemMedChem 7 (10), pp. 1775 - 1783 (2012)
  80. Journal Article
    Jelen, S.; Wacker, S.; Aponte-Santamaria, C. A.; Skott, M.; Rojek, A.; Johanson, U.; Kjellbom, P.; Nielsen, S.; de Groot, B. L.; Ruetzler, M.: Aquaporin-9 protein is the primary route of hepatocyte glycerol uptake for glycerol gluconeogenesis in mice. Journal of Biological Chemistry 286 (52), pp. 44319 - 44325 (2011)
  81. Journal Article
    Ban, D.; Funk, M.; Gulich, R.; Egger, D.; Sabo, T. M.; Walter, K. F. A.; Fenwick, R. B.; Giller, K.; Pichierri, F.; de Groot, B. L. et al.; Lange, O. F.; Grubmüller, H.; Salvatella, X.; Wolf, M.; Loidl, A.; Kree, R.; Becker, S.; Lakomek, N. A.; Lee, D.; Lunkenheimer, P.; Griesinger, C.: Kinetics of conformational sampling in ubiquitin. Angewandte Chemie-International Edition 50 (48), pp. 11437 - 11440 (2011)
  82. Journal Article
    Seeliger, D.; Buelens, F. P.; Götte, M.; de Groot, B. L.; Grubmüller, H.: Towards computional specificity screening of DNA-binding proteins. Nucleic Acids Research 39 (19), pp. 8281 - 8290 (2011)
  83. Journal Article
    Kutzner, C.; Grubmüller, H.; de Groot, B. L.; Zachariae, U.: Computational Electrophysiology: The molecular dynamics of ion channel Permeation and selectivity in atomistic detail. Biophysical Journal 101 (4), pp. 809 - 817 (2011)
  84. Journal Article
    Boukharta, L.; Keranen, H.; Stary-Weinzinger, A.; Wallin, G.; de Groot, B. L.; Aqvist, J.: Computer simulations of structure-activity relationships for hERG channel blockers. Biochemistry 50 (27), pp. 6146 - 6156 (2011)
  85. Journal Article
    Hub, J. S.; de Groot, B. L.: Comment on “Molecular selectivity in aquaporin channels studied by the 3D-RISM theory”. The Journal of Physical Chemistry B 115 (25), pp. 8364 - 8366 (2011)
  86. Journal Article
    Matthes, D.; Gapsys, V.; Daebel, V.; de Groot, B. L.: Mapping the conformational dynamics and pathways of spontaneous steric zipper peptide oligomerization. Plos One 6 (5) (2011)
  87. Journal Article
    de Groot, B. L.; Hub, J. S.: A decade of debate: Significance of CO2 permeation through membrane channels still controversial. Chemphyschem 12 (5), pp. 1021 - 1022 (2011)
  88. Journal Article
    Villinger, S.; Briones, R.; Giller, K.; Zachariä, U.; Lange, A.; de Groot, B. L.; Griesinger, C.; Becker, S.; Zweckstetter, M.: Functional dynamics in the voltage-dependent anion channel. Proceedings of the National Academy of Sciences of the United States of America 107 (52), pp. 22546 - 22551 (2010)
  89. Journal Article
    Hub, J. S.; Aponte-Santamaria, C.; Grubmüller, H.; de Groot, B. L.: Voltage-regulated water flux through aquaporin channels in silico. Biophysical Journal 99 (12), pp. L97 - L99 (2010)
  90. Journal Article
    Hub, J. S.; de Groot, B. L.; van der Spoel, D.: g_wham-A free weighted histogram analysis implementation including robust error and autocorrelation estimates. Journal of Chemical Theory and Computation 6 (12), pp. 3713 - 3720 (2010)
  91. Journal Article
    Lopez Cacales, J. J.; Oliviera Costa, S. D.; de Groot, B. L.; Walters, D. E.: Binding of glutamate to the umami receptor. Biophysical Chemistry 152 (1-3), pp. 139 - 144 (2010)
  92. Journal Article
    Hub, J. S.; Winkler, F. K.; Merrick, M.; de Groot, B. L.: Potentials of mean force and permeabilities for carbon dioxide, ammonia, and water flux across a Rhesus protein channel and lipid membranes. Journal of American Chemical Society 132 (38), pp. 13251 - 13263 (2010)
  93. Journal Article
    Lange, O. F.; van der Spoel, D.; de Groot, B. L.: Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data. Biophysical Journal 99 (2), pp. 647 - 655 (2010)
  94. Journal Article
    Seeliger, D.; de Groot, B. L.: Protein thermostability calculations using alchemical free energy simulations. Biophysical Journal 98 (10), pp. 2309 - 2316 (2010)
  95. Journal Article
    Hub, J. S.; Kubitzki, M. B.; de Groot, B. L.: Spontaneous quaternary and tertiary T-R transitions of human hemoglobin in molecular dynamics simulation. PLoS Computational Biology 6, e1000774 (2010)
  96. Journal Article
    Seeliger, D.; de Groot, B. L.: Ligand docking and binding site analysis with PyMOL and Autodock/Vina. Journal of Computer-Aided Molecular Design 24 (5), pp. 417 - 422 (2010)
  97. Journal Article
    de Boer, T. P.; Nalos, L.; Stary, A.; Kok, B.; Houtman, M. J. C.; Antoons, G.; van Feen, T. A. B.; Beekman, J. D. M.; de Groot, B. L.; Opthof, T. et al.; Rook, M. B.; Vos, M. A.; van der Heyden, M. A. G.: The anti-protozoal drug pentamidine blocks KIR2.x-mediated inward rectifier current by entering the cytoplasmic pore region of the channel. British Journal of Pharmacology 159 (7), pp. 1532 - 1541 (2010)
  98. Journal Article
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