Zeitschriftenartikel (145)

  1. Zeitschriftenartikel
    Aponte-Santamaria, C.; Hub, J. S.; de Groot, B. L.: Dynamics and energetics of solute permeation through the Plasmodium falciparum aquaglyceroporin. Physical Chemistry Chemical Physics 12 (35), S. 10246 - 10254 (2010)
  2. Zeitschriftenartikel
    Fenton, R. A.; Moeller, H. B.; Nielsen, S.; de Groot, B. L.; Rutzler, M.: A plate reader-based method for cell water permeability measurement. American Journal of Physiology 298 (1), S. F224 - F230 (2010)
  3. Zeitschriftenartikel
    Hub, J. S.; de Groot, B. L.: Detection of functional modes in protein dynamics. PLoS Computational Biology 5 (8), e1000480 (2009)
  4. Zeitschriftenartikel
    Matthes, D.; de Groot, B. L.: Secondary structure propensities in peptide folding simulations: A systematic comparison of molecular mechanics interaction schemes. Biophysical Journal 97 (2), S. 599 - 608 (2009)
  5. Zeitschriftenartikel
    Joshi, H.; Jedrzejas, M. J.; de Groot, B. L.: Domain motions of hyaluronan lyase underlying processive hyaluronan translocation. Proteins: Structure, Function and Bioinformatics 76 (1), S. 30 - 46 (2009)
  6. Zeitschriftenartikel
    Stegmann, C. M.; Seeliger, D.; Sheldrick, G. M.; de Groot, B. L.; Wahl, M. C.: The thermodynamic influence of trapped water molecules on a protein-ligand interaction. Angewandte Chemie - International Edition 48 (28), S. 5207 - 5210 (2009)
  7. Zeitschriftenartikel
    Seeliger, D.; de Groot, B. L.: tCONCOORD-GUI: Visually supported conformational sampling of bioactive molecules. Journal of Computational Chemistry 30 (7), S. 1160 - 1166 (2009)
  8. Zeitschriftenartikel
    Portella, G.; de Groot, B. L.: Determinants of water permeability through nanoscopic hydrophilic channels. Biophysical Journal 96 (3), S. 925 - 938 (2009)
  9. Zeitschriftenartikel
    Benedix, A.; Becker, C. M.; de Groot, B. L.; Caflisch, A.; Boeckmann, R. A.: Predicting free energy changes using structural ensembles. Nature Methods 6 (1), S. 3 - 4 (2009)
  10. Zeitschriftenartikel
    Lakomek, N. A.; Lange, O.; Walter, K.; Fares, C.; Egger, D.; Lunkenheimer, P.; Meiler, J.; Grubmueller, H.; Becker, S.; de Groot, B. L. et al.; Griesinger, C.: Residual dipolar couplings as a tool to study molecular recognition of ubiquitin. Biochemical Society Transactions 36 (6), S. 1433 - 1437 (2008)
  11. Zeitschriftenartikel
    Kubitzki, M. B.; de Groot, B. L.: The atomistic mechanism of conformational transition in adenylate kinase: a TEE-REX molecular dynamics study. Structure 16 (8), S. 1175 - 1182 (2008)
  12. Zeitschriftenartikel
    Lakomek, N. A.; Walter, K.; Fares, C.; Lange, O.; de Groot, B. L.; Grubmueller, H.; Brueschweiler, R.; Munk, A.; Becker, S.; Meiler, J. et al.; Griesinger, C.: Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics. Journal of Biomolecular NMR 41 (3), S. 139 - 155 (2008)
  13. Zeitschriftenartikel
    Lange, O.F.; Lakomek, N. A.; Fares, C.; Schroeder, G. F.; Walter, K.; Becker, S.; Meiler, J.; Grubmueller, H.; Griesinger, C.; de Groot, B. L.: Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science 320 (5882), S. 1471 - 1475 (2008)
  14. Zeitschriftenartikel
    Zachariae, U.; Grubmueller, H.: Importin-β: structural and dynamic determinants of a molecular spring. Structure 16 (6), S. 906 - 915 (2008)
  15. Zeitschriftenartikel
    Zachariae, U.; Schneider, R.; Velisetty, P.; Lange, A.; Seeliger, D.; Wacker, S.; Karimi-Nejad, J.; Vriend, G.; Becker, S.; Pongs, O. et al.; Baldus, M.; de Groot, B. L.: The molecular mechanism of toxin-induced conformational changes in a potassium channel: relation to C-type inactivation. Structure 16 (5), S. 747 - 754 (2008)
  16. Zeitschriftenartikel
    Hartmann, C.; Chami, M.; Zachariae, U.; de Groot, B. L.; Engel, A.; Gruetter, M. G.: Vacuolar protein sorting: two different functional states of the AAA-ATPase Vps4p. Journal of Molecular Biology 377 (2), S. 352 - 363 (2008)
  17. Zeitschriftenartikel
    Hub, J.; de Groot, B. L.: Mechanism of selectivity in aquaporins and aquaglyceroporins. Proceedings of the National Acadamy of Sciences of the United States of America 105 (4), S. 1198 - 1203 (2008)
  18. Zeitschriftenartikel
    Boeckmann, R. A.; de Groot, B. L.; Kakorin, S.; Neumann, E.; Grubmueller, H.: Kinetics, statistics, and energetics of lipid membrane electroporation studied by molecular dynamics simulations. Biophysical Journal 95, S. 1837 - 1850 (2008)
  19. Zeitschriftenartikel
    Mueller, E. M.; Hub, J.; Grubmueller, H.; de Groot, B. L.: Is TEA an inhibitor for human Aquaporin-1? Pfluegers Archiv 456 (4), S. 663 - 669 (2008)
  20. Zeitschriftenartikel
    Portella, G.; Hub, J.; Vesper, M. D.; de Groot, B. L.: Not only enthalpy: large entropy contribution to ion permeation barriers in single-file channels. Biophysical Journal 95, S. 2275 - 2282 (2008)
  21. Zeitschriftenartikel
    Seeliger, D.; Haas, J.; de Groot, B. L.: Geometry-based sampling of conformational transitions in proteins. Structure 15 (11), S. 1482 - 1492 (2007)
  22. Zeitschriftenartikel
    Hub, J. S.; Salditt, T.; Rheinstaedter, M. C.; de Groot, B. L.: Short-range order and collective dynamics of DMPC bilayers: a comparison between molecular dynamics simulations, X-ray, and neutron scattering experiments. Biophysical Journal 93 (9), S. 3156 - 3168 (2007)
  23. Zeitschriftenartikel
    Vermeer, L. S.; de Groot, B. L.; Reat, V.; Milon, A.; Czaplicki, J.: Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments. European Biophysical Journal 36 (8), S. 919 - 931 (2007)
  24. Zeitschriftenartikel
    Seeliger, D.; de Groot, B. L.: Atomic contacts in protein structures. A detailed analysis of atomic radii, packing, and overlaps. Proteins-Structure Function and Bioinformatics 68 (3), S. 595 - 601 (2007)
  25. Zeitschriftenartikel
    Portella, G.; Pohl, P.; de Groot, B. L.: Invariance of single-file water mobility in gramicidin-like peptidic pores as function of pore length. Biophysical Journal 92 (11), S. 3930 - 3937 (2007)
  26. Zeitschriftenartikel
    Kubitzki, M. B.; de Groot, B. L.: Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange. Biophysical Journal 92, S. 4262 - 4270 (2007)
  27. Zeitschriftenartikel
    Kutzner, C.; van der Spoel, D.; Fechner, M.; Lindahl, E.; Schmitt, U. W.; de Groot, B. L.; Grubmueller, H.: Speeding up parallel GROMACS on high-latency networks. Journal of Computational Chemistry 28 (12), S. 2075 - 2084 (2007)
  28. Zeitschriftenartikel
    Takamori, S.; Holt, M.; Stenius, K.; Lemke, E.; Groenborg, M.; Riedel, D.; Urlaub, H.; Schenck, S.; Bruegger, B.; Ringler, P. et al.; Mueller, S.; Rammner, B.; Graeter, F.; Hub, J. S.; de Groot, B. L.; Mieskes, G.; Moriyama, Y.; Klingauf, J.; Grubmueller, H.; Heuser, J.; Wieland, F.; Jahn, R.: Molecular anatomy of a trafficking organelle. Cell 127 (4), S. 831 - 846 (2006)
  29. Zeitschriftenartikel
    Graeter, F.; de Groot, B. L.; Jiang, H.; Grubmueller, H.: Ligand-release pathways in the pheromone-binding protein of Bombyx mori. Structure 14 (10), S. 1567 - 1576 (2006)
  30. Zeitschriftenartikel
    Zachariae, U.; Grubmueller, H.: A highly strained nuclear conformation of the exportin Cse1p revealed by molecular dynamics simulations. Structure 14 (9), S. 1469 - 1478 (2006)
  31. Zeitschriftenartikel
    Hub, J. S.; de Groot, B. L.: Does CO2 permeate through Aquaporin-1? Biophysical Journal 91 (3), S. 842 - 848 (2006)
  32. Zeitschriftenartikel
    Detmers, F. J. M.; de Groot, B. L.; Mueller, E. M.; Hinton, A.; Konings, I. B. M.; Sze, M.; Flitsch, S. L.; Grubmueller, H.; Deen, P. M. T.: Quaternary Ammonium Compounds as Water Channel Blockers. Journal of Biological Chemistry 281 (20), S. 14207 - 14214 (2006)
  33. Zeitschriftenartikel
    Rigden, D. J.; Littlejohn, J. E.; Joshi, H.; de Groot, B. L.; Jedrzejas, M. J.: Alternate Structural Conformations of Streptococcus pneumoniae Hyaluronan Lyase: Insights into Enzyme Flexibility and Underlying Molecular Mechanism of Action. Journal of Molecular Biology 358 (4), S. 1165 - 1178 (2006)
  34. Zeitschriftenartikel
    Rigden, D. J.; Liilejohn, J. E.; Joshi, H.; de Groot, B. L.; Jedrzejas, M. J.: Alternate structural conformations of Streptococcus pneumoniae hyaluronan lyase: Insights into enzyme flexibility and underlying molecular mechanism of action. Journal of Molecular Biology 358 (4), S. 1165 - 1178 (2006)
  35. Zeitschriftenartikel
    de Groot, B. L.; Boeckmann, R. A.; Grubmueller, H.: Proteindynamik-Simulationen. Molekulare Nanomaschinen unter der Lupe. Physik in unserer Zeit 37, S. 73 - 79 (2006)
  36. Zeitschriftenartikel
    Saparov, S. M.; Pfeifer, J. R.; Al-Momani, L.; Portella, G.; de Groot, B. L.; Koert, U.; Pohl, P.: Mobility of a One-Dimensional Confined File of Water Molecules as a Function of File Length. Physical Review Letters 96, 148101 (2006)
  37. Zeitschriftenartikel
    Seeliger, D.; de Groot, B. L.: Prediction of protein flexibility from geometrical constraints. Bio Tech Interantional 18, S. 20 - 22 (2006)
  38. Zeitschriftenartikel
    Soerensen, J. B.; Wiederhold, K.; Mueller, E. M.; Milosevic, I.; Nagy, G.; de Groot, B. L.; Grubmueller, H.; Fasshauer, D.: Sequential N-to C-terminal SNARE complex assembly drives priming and fusion of secretory vesicles. EMBO Journal 25, S. 955 - 966 (2006)
  39. Zeitschriftenartikel
    Zachariae, U.; Grubmüller, H.: Prediction of a RanGTP-induced conformational switch in the exportin CAS/Cse1p by molecular dynamics simulations. MPIbpc News 5, S. 1 - 6 (2006)
  40. Zeitschriftenartikel
    Nagy, G.; Milosevic, I.; Fasshauer, D.; Mueller, E. M.; de Groot, B. L.; Lang, T.; Wilson, M. C.; Soerensen, J. B.: Alternative splicing of SNAP-25 regulates secretion through nonconservative substitutions in the SNARE domain. Molecular Biology of the Cell 16 (12), S. 5675 - 5685 (2005)
  41. Zeitschriftenartikel
    Heise, H.; Luca, S.; de Groot, B. L.; Grubmueller, H.; Baldus, M.: Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations. Biophysical Journal 89 (3), S. 2113 - 2120 (2005)
  42. Zeitschriftenartikel
    Kukulski, W.; Schenk, A. D.; Johanson, U.; Braun, T.; de Groot, B. L.; Fotiadis, D.; Kjellbom, P.; Engel, A.: The 5 angstrom structure of heterologously expressed plant aquaporin SoPIP2;1. Journal of Molecular Biology 350 (4), S. 611 - 616 (2005)
  43. Zeitschriftenartikel
    Schenk, A. D.; Werten, P. J. L.; Scheuring, S.; de Groot, B. L.; Müller, S. A.; Stahlberg, H.; Philippsen, A.; Engel, A.: The 4.5 Å structure of human AQP2. Journal of Molecular Biology 350 (2), S. 278 - 289 (2005)
  44. Zeitschriftenartikel
    de Groot, B. L.; Grubmueller, H.: The dynamics and energetics of water permeation and proton exclusion in aquaporins. Current Opinion in Structural Biology 15 (2), S. 176 - 183 (2005)
  45. Zeitschriftenartikel
    Lange, O.; Grubmueller, H.; de Groot, B. L.: Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone motions. Angewandte Chemie-International Edition 44 (22), S. 3394 - 3399 (2005)
  46. Zeitschriftenartikel
    de Groot, B. L.; Grubmueller, H.: Aquaporine: Die perfekten Wasserfilter der Zelle. Biospektrum 10 (4), S. 384 - 386 (2004)

Buchkapitel (7)

  1. Buchkapitel
    Aldeghi, M.; de Groot, B. L.; Gapsys, V.: Accurate calculation of free energy changes upon amino acid mutation. In: Computational Methods in Protein Evolution, S. 19 - 47 (Hg. Sikosek, T.). Springer Nature, New York (2019)
  2. Buchkapitel
    Kubitzki, M. B.; de Groot, B. L.; Seeliger, D.: Protein dynamics: From structure to function. In: From protein structure to function with bioinformatics, S. 393 - 425 (Hg. Rigden, D. J.). Springer, Dordrecht (2017)
  3. Buchkapitel
    Gapsys, V.; Michielssens, S.; Peters, J. H.; de Groot, B.; Leonov, H.: Calculation of binding free energies. In: Molecular Modeling of Proteins, S. 173 - 209 (Hg. Kukol, A.). Humana Pr.; Springer, New York, N.Y. (2015)
  4. Buchkapitel
    Hub, J.; Grubmuller, H.; de Groot, B. L.: Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations? In: Aquaporins, S. 57 - 76 (Hg. Beitz, E.). Springer, Berlin (2009)
  5. Buchkapitel
    Kubitzki, M. B.; de Groot, B. L.; Seeliger, D.: Protein dynamics: From structure to function. In: From Protein Structure to Function with Bioinformatics, S. 217 - 249 (Hg. Rigden, D.J.). Springer, Dordrecht (2009)
  6. Buchkapitel
    Hayward, S.; de Groot, B. L.: Normal modes and essential dynamics. In: Molecular modeling of proteins, S. 89 - 106 (Hg. Kukol, A.). Humana Pr., Totowa, N. Y. (2008)
  7. Buchkapitel
    Kutzner, C.; van der Spoel, D.; Fechner, M.; Lindahl, E.; Schmitt, U. W.; de Groot, B. L.; Grubmueller, H.: Improved GROMACS scaling on ethernet switched clusters. In: Recent advances in parallel virtual machine and message passing interface. 13th European PVM/MPI User`s Group meeting, Bonn, Germany, September 17-20, 2006, S. 404 - 405 (Hg. Mohr, B.; Larsson, T. J.; Worringen, J.; Dongarra, J.). Springer, Berlin (2006)
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