Publikationen

2.

Zeitschriftenartikel

Gapsys, V.; Yildirim, A.; Aldeghi, M.; Khalak, Y.; van der Spoel, D.; de Groot, B. L.: Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches. Communications Chemistry 4, 61 (2021)

MPG.PuRe

3.

Zeitschriftenartikel

Roy, R. N.; Hendriks, K.; Kopec, W.; Abdolvand, S.; Weiss, K. L.; de Groot, B. L.; Lange, A.; Sun, H.; Coates, L.: Structural plasticity of the selectivity filter in a nonselective ion channel. IUCrJ 8 (3), S. 421 - 430 (2021)

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4.

Zeitschriftenartikel

Baumann, H. M.; Gapsys, V.; de Groot, B. L.; Mobley, D. L.: Challenges encountered applying equilibrium and nonequilibrium binding free energy calculations. Journal of Physical Chemistry B 125 (17), S. 4241 - 4261 (2021)

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5.

Zeitschriftenartikel

Werner, M.; Gapsys, V.; de Groot, B. L.: One plus one makes three: Triangular coupling of correlated amino acid mutations. Journal of Physical Chemistry Letters 12 (12), S. 3195 - 3201 (2021)

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6.

Zeitschriftenartikel

Buelens, F. P.; Leonov, H.; de Groot, B. L.; Grubmüller, H.: ATP-magnesium coordination: Protein structure-based force field evaluation and corrections. Journal of Chemical Theory and Computation 17 (3), S. 1922 - 1930 (2021)

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7.

Zeitschriftenartikel

Daday, C.; de Groot, B. L.: Lipid–protein forces predict conformational changes in a mechanosensitive channel. European Biophysics Journal 50 (2), S. 181 - 186 (2021)

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8.

Zeitschriftenartikel

de Groot, B. L.; Janshoff, A.; Steinem, C.; Zweckstetter, M.: Special issue: Multicomponent lipid membranes—how molecular organisation leads to function. European Biophysics Journal 50 (2), S. 107 - 108 (2021)

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9.

Zeitschriftenartikel

Najbauer, E.; Becker, S.; Giller, K.; Zweckstetter, M.; Lange, A.; Steinem, C.; de Groot, B. L.; Griesinger, C.; Andreas, L. B.: Structure, gating and interactions of the voltage-dependent anion channel. European Biophysics Journal 50 (2), S. 159 - 172 (2021)

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10.

Zeitschriftenartikel

Zhang, Y.; Daday, C.; Gu, R. X.; Cox, C. D.; Martinac, B.; de Groot, B. L.; Walz, T.: Visualization of the mechanosensitive ion channel MscS under membrane tension. Nature 590 (7846), S. 509 - 514 (2021)

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11.

Zeitschriftenartikel

Khalak, Y.; Tresadern, G.; de Groot, B. L.; Gapsys, V.: Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software. Journal of Computer-Aided Molecular Design 35 (1), S. 49 - 61 (2021)

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12.

Zeitschriftenartikel

Rabe von Pappenheim, F.; Aldeghi, M.; Shome, B.; Begley, T.; de Groot, B. L.; Tittmann, K.: Structural basis for antibiotic action of the B1 antivitamin 2′-methoxy-thiamine. Nature Chemical Biology 16 (11), S. 1237-1245 (2020)

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13.

Zeitschriftenartikel

Gapsys, V.; de Groot, B. L.: On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size. eLife 9, e57589 (2020)

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14.

Zeitschriftenartikel

Langan, P. S.; Vandavasi, V. G.; Kopec, W.; Sullivan, B.; Afonne, P. V.; Weiss, K. L.; de Groot, B. L.; Coates, L.: The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation. IUCrJ 7 (5), S. 835 - 843 (2020)

MPG.PuRe

15.

Zeitschriftenartikel

Schubeis, T.; Le Marchand, T.; Daday, C.; Kopec, W.; Tekwani Movellan, K.; Stanek, J.; Schwarzer, T. S.; Castiglione, K.; de Groot, B. L.; Pintacuda, G. et al.; Andreas, L. B.: A β-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkL. Proceedings of the National Academy of Sciences of the United States of America 117 (35), S. 21014 - 21021 (2020)

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16.

Zeitschriftenartikel

Bastys, T.; Gapsys, V.; Walter, H.; Heger, E.; Doncheva, N. T.; Kaiser, R.; de Groot, B. L.; Kalinina, O. V.: Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors. Retrovirology 17, 13 (2020)

MPG.PuRe

17.

Zeitschriftenartikel

Gu, R. X.; de Groot, B. L.: Lipid-protein interactions modulate the conformational equilibrium of a potassium channel. Nature Communications 11, 2162 (2020)

MPG.PuRe

18.

Zeitschriftenartikel

Rizzi, A.; Jensen, T.; Slochower, D. R.; Aldeghi, M.; Gapsys, V.; Ntekoumes, D.; Bosisio, S.; Papadourakis, M.; Henriksen, N. M.; de Groot, B. L. et al.; Cournia, Z.; Dickson, A.; Michel, J.; Gilson, M. K.; Shirts, M. R.; Mobley, D. L.; Chodera, J. D.: The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations. Journal of Computer-Aided Molecular Design 34 (5), S. 601 - 633 (2020)

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pre-print

19.

Zeitschriftenartikel

Gapsys, V.; Khabiri, M.; de Groot, B. L.; Freddolino, P. L.: Comment on "Deficiencies in molecular dynamics simulation-based prediction of protein-DNA binding free energy landscapes". The Journal of Physical Chemistry B 124 (6), S. 1115 - 1123 (2020)

MPG.PuRe

20.

Zeitschriftenartikel

de Maré, S. W.; Venskutonytė, R.; Eltschkner, S.; de Groot, B. L.; Lindkvist-Petersson, K.: Structural basis for glycerol efflux and selectivity of human Aquaporin 7. Structure 28 (2), S. 215 - 222 (2020)

MPG.PuRe

21.

Zeitschriftenartikel

Gapsys, V.; Perez-Benito, L.; Aldeghi, M.; Seeliger, D.; Van Vlijmen, H.; Tresadern, G.; de Groot, B. L.: Large scale relative protein ligand binding affinities using non-equilibrium alchemy. Chemical Science 11 (4), S. 1140 - 1152 (2020)

MPG.PuRe

22.

Zeitschriftenartikel

Smith, C. A.; Mazur, A.; Rout, A. K.; Becker, S.; Lee, D.; de Groot, B. L.; Griesinger, C.: Enhancing NMR derived ensembles with kinetics on multiple timescales. Journal of Biomolecular NMR 74 (1), S. 27 - 43 (2020)

MPG.PuRe

23.

Zeitschriftenartikel

Elisee, E.; Gapsys, V.; Mele, N.; Chaput, L.; Selwa, E.; de Groot, B. L.; Iorga, B. I.: Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset. Journal of Computer-Aided Molecular Design 33, S. 1031 - 1043 (2019)

MPG.PuRe

24.

Zeitschriftenartikel

Kopec, W.; Rothberg, B. S.; de Groot, B. L.: Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling. Nature Communications 10, 5366 (2019)

MPG.PuRe

25.

Zeitschriftenartikel

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), S. 2418 - 2431 (2019)

MPG.PuRe

26.

Zeitschriftenartikel

Aldeghi, M.; Gapsys, V.; de Groot, B. L.: Predicting kinase inhibitor resistance: Physics-based and data-driven approaches. ACS Central Science 5 (8), S. 1468 - 1474 (2019)

MPG.PuRe

27.

Zeitschriftenartikel

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), eaaw6756 (2019)

MPG.PuRe

28.

Zeitschriftenartikel

Gapsys, V.; de Groot, B. L.: Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'. eLife 8, e44718 (2019)

MPG.PuRe

29.

Zeitschriftenartikel

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), S. 816 - 827 (2019)

MPG.PuRe

30.

Zeitschriftenartikel

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), S. 1658 - 1666 (2019)

MPG.PuRe

31.

Zeitschriftenartikel

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), 925 (2019)

MPG.PuRe

32.

Zeitschriftenartikel

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), S. 875 - 880 (2019)

MPG.PuRe

33.

Zeitschriftenartikel

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), S. 780 - 794 (2019)

MPG.PuRe

34.

Zeitschriftenartikel

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 K_v1 channels. Proceedings of the National Academy of Sciences of the United States of America 116 (3), S. 1059 - 1064 (2019)

MPG.PuRe

35.

Zeitschriftenartikel

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), S. 4 - 11 (2019)

MPG.PuRe

36.

Zeitschriftenartikel

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), S. 698 - 707 (2019)

MPG.PuRe

37.

Zeitschriftenartikel

Gu, R. X.; Baoukina, S.; Tieleman, D. P.: Cholesterol flip-flop in heterogeneous membranes. Journal of Chemical Theory and Computation 15 (3), S. 2064 - 2070 (2019)

MPG.PuRe

38.

Zeitschriftenartikel

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)

MPG.PuRe

39.

Zeitschriftenartikel

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), S. 858 - 869 (2019)

MPG.PuRe

40.

Zeitschriftenartikel

Aldeghi, M.; Gapsys, V.; de Groot, B. L.: Accurate estimation of ligand binding affinity changes upon protein mutation. ACS Central Science 4 (12), S. 1708 - 1718 (2018)

MPG.PuRe

41.

Zeitschriftenartikel

Brennecke, J. T.; de Groot, B. L.: Quantifying asymmetry of multimeric proteins. The Journal of Physical Chemistry A 122 (39), S. 7924 - 7930 (2018)

MPG.PuRe

42.

Zeitschriftenartikel

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), S. 813 - 820 (2018)

MPG.PuRe

43.

Zeitschriftenartikel

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), S. 3397 - 3408 (2018)

MPG.PuRe

44.

Zeitschriftenartikel

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, 6886 (2018)

MPG.PuRe

45.

Zeitschriftenartikel

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, S. 85 - 92 (2018)

MPG.PuRe

46.

Zeitschriftenartikel

Brennecke, J. T.; de Groot, B. L.: Mechanism of mechanosensitive gating of the TREK-2 potassium channel. Biophysical Journal 114 (6), S. 1336 - 1343 (2018)

MPG.PuRe

47.

Zeitschriftenartikel

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, 717 (2018)

MPG.PuRe

48.

Zeitschriftenartikel

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), S. 2791 - 2808 (2017)

MPG.PuRe

49.

Zeitschriftenartikel

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), S. 6275 - 6289 (2017)

MPG.PuRe

50.

Zeitschriftenartikel

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, S. 81 - 91 (2017)

MPG.PuRe

51.

Zeitschriftenartikel

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, 4016 (2017)

MPG.PuRe

52.

Zeitschriftenartikel

Machtens, J. P.; Briones, R.; Alleva, C.; de Groot, B. L.; Fahlke, C.: Gating charge calculations by computational electrophysiology simulations. Biophysical Journal 112 (7), S. 1396 - 1405 (2017)

MPG.PuRe

53.

Zeitschriftenartikel

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), S. 953 - 965 (2017)

MPG.PuRe

54.

Zeitschriftenartikel

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, 124 (2017)

MPG.PuRe

55.

Zeitschriftenartikel

Gapsys, V.; de Groot, B. L.: pmx Webserver: A user friendly interface for alchemistry. Journal of Chemical Information and Modeling 57 (2), S. 109 - 114 (2017)

MPG.PuRe

56.

Zeitschriftenartikel

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), S. 71 - 73 (2017)

MPG.PuRe

57.

Zeitschriftenartikel

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), S. 1223 - 1234 (2016)

MPG.PuRe

58.

Zeitschriftenartikel

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), S. 10358 - 10363 (2016)

MPG.PuRe

59.

Zeitschriftenartikel

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, 33156 (2016)

MPG.PuRe

60.

Zeitschriftenartikel

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), S. 19184 - 19195 (2016)

MPG.PuRe

61.

Zeitschriftenartikel

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), S. 1741 - 1752 (2016)

MPG.PuRe

62.

Zeitschriftenartikel

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), S. 7364 - 7368 (2016)

MPG.PuRe

63.

Zeitschriftenartikel

Singer, M.; Krivobokova, T.; Munk, A.; De Groot, B. L.: Partial least squares for dependent data. Biometrika 103 (2), S. 351 - 362 (2016)

MPG.PuRe

64.

Zeitschriftenartikel

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), e1002411 (2016)

MPG.PuRe

65.

Zeitschriftenartikel

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), S. 3269 - 3274 (2016)

MPG.PuRe

66.

Zeitschriftenartikel

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), S. 937 - 949 (2016)

MPG.PuRe

67.

Zeitschriftenartikel

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), S. 2309 - 2318 (2015)

MPG.PuRe

68.

Zeitschriftenartikel

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), e0143399 (2015)

MPG.PuRe

69.

Zeitschriftenartikel

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), S. 5513 - 5524 (2015)

MPG.PuRe

70.

Zeitschriftenartikel

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), S. 299 - 307 (2015)

MPG.PuRe

71.

Zeitschriftenartikel

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), S. 1990 - 2008 (2015)

MPG.PuRe

72.

Zeitschriftenartikel

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), S. 12390 - 12395 (2015)

MPG.PuRe

73.

Zeitschriftenartikel

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, 1507.00898v1 (2015)

MPG.PuRe

pre-print

74.

Zeitschriftenartikel

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), S. F1324 - F1334 (2015)

MPG.PuRe

75.

Zeitschriftenartikel

Michielssens, S.; de Groot, B. L.; Grubmüller, H.: Binding affinities controlled by shifting conformational equilibria: Opportunities and limitations. Biophysical Journal 108 (10), S. 2585 - 2590 (2015)

MPG.PuRe

76.

Zeitschriftenartikel

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), S. 348 - 354 (2015)

MPG.PuRe

77.

Zeitschriftenartikel

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), S. 542 - 553 (2015)

MPG.PuRe

78.

Zeitschriftenartikel

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), S. 207 - 210 (2015)

MPG.PuRe

79.

Zeitschriftenartikel

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), S. 352 - 355 (2014)

MPG.PuRe

80.

Zeitschriftenartikel

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), S. 10367 - 10371 (2014)

MPG.PuRe

81.

Zeitschriftenartikel

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), S. 362 - 376 (2014)

MPG.PuRe

82.

Zeitschriftenartikel

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), S. 381 - 390 (2014)

MPG.PuRe

83.

Zeitschriftenartikel

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), S. 2162 - 2174 (2013)

MPG.PuRe

84.

Zeitschriftenartikel

Gapsys, V.; de Groot, B. L.; Briones, R.: Computational analysis of local membrane properties. Journal of Computer-Aided Molecular Design 27 (10), S. 845 - 858 (2013)

MPG.PuRe

85.

Zeitschriftenartikel

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), S. 7397 - 7404 (2013)

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Vesper, M. D.; de Groot, B. L.: Collective dynamics underlying allosteric transitions in hemoglobin. PLoS Computational Biology 9 (9), e1003232 (2013)

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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), S. 1101 - 1112 (2013)

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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), e1003058 (2013)

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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), S. 246 - 260 (2013)

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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), S. 4586 - 4591 (2013)

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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), S. 249 - 256 (2013)

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Gapsys, V.; de Groot, B. L.: Optimal superpositioning of flexible molecule ensemble. Biophysical Journal 104 (1), S. 196 - 207 (2013)

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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), e1002704 (2012)

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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), S. 1540 - 1549 (2012)

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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), S. 786 - 796 (2012)

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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), S. 390 - 416 (2012)

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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), S. 8350 - 8357 (2012)

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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), e41023 (2012)

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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), S. 2373 - 2382 (2012)

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