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Journal Article (121)

  1. 1.
    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 (2018)
  2. 2.
    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)
  3. 3.
    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 (2018)
  4. 4.
    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)
  5. 5.
    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)
  6. 6.
    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 (2018)
  7. 7.
    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)
  8. 8.
    Brennecke, J. T.; de Groot, B. L.: Quantifying asymmetry of multimeric proteins. The Journal of Physical Chemistry A 122 (39), pp. 7924 - 7930 (2018)
  9. 9.
    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)
  10. 10.
    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)
  11. 11.
    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)
  12. 12.
    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 (2017)
  13. 13.
    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)
  14. 14.
    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)
  15. 15.
    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)
  16. 16.
    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)
  17. 17.
    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)
  18. 18.
    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 (2016)
  19. 19.
    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 (2016)
  20. 20.
    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)
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