Publications

102.

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)

MPG.PuRe

103.

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)

MPG.PuRe

104.

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)

MPG.PuRe

105.

Journal Article

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

MPG.PuRe

106.

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)

MPG.PuRe

107.

Journal Article

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

MPG.PuRe

108.

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)

MPG.PuRe

109.

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), e1003058 (2013)

MPG.PuRe

110.

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)

MPG.PuRe

111.

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)

MPG.PuRe

112.

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)

MPG.PuRe

113.

Journal Article

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

MPG.PuRe

114.

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), e1002704 (2012)

MPG.PuRe

115.

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)

MPG.PuRe

116.

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)

MPG.PuRe

117.

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)

MPG.PuRe

118.

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)

MPG.PuRe

119.

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), e41023 (2012)

MPG.PuRe

120.

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)

MPG.PuRe

121.

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)

MPG.PuRe

122.

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)

MPG.PuRe

123.

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)

MPG.PuRe

124.

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)

MPG.PuRe

125.

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)

MPG.PuRe

126.

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)

MPG.PuRe

127.

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)

MPG.PuRe

128.

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)

MPG.PuRe

129.

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)

MPG.PuRe

130.

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), e19129 (2011)

MPG.PuRe

131.

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)

MPG.PuRe

132.

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)

MPG.PuRe

133.

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)

MPG.PuRe

134.

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)

MPG.PuRe

135.

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)

MPG.PuRe

136.

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)

MPG.PuRe

137.

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)

MPG.PuRe

138.

Journal Article

Seeliger, D.; de Groot, B. L.: Protein thermostability calculations using alchemical free energy simulations. Biophysical Journal 98 (10), pp. 2309 - 2316 (2010)

MPG.PuRe

139.

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)

MPG.PuRe

140.

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)

MPG.PuRe

141.

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 K_IR2.x-mediated inward rectifier current by entering the cytoplasmic pore region of the channel. British Journal of Pharmacology 159 (7), pp. 1532 - 1541 (2010)

MPG.PuRe

142.

Journal Article

Stary, A.; Wacker, S.; Boukharta, L.; Zachariae, U.; Karimi-Nejad, Y.; Aqvist, J.; Vriend, G.; de Groot, B. L.: Toward a consensus model of the hERG potassium channel. ChemMedChem 5 (3), pp. 455 - 467 (2010)

MPG.PuRe

143.

Journal Article

Seeliger, D.; de Groot, B. L.: Conformational transitions upon ligand binding: Holo-structure prediction from apo conformations. PLoS Computational Biology 6 (1), e1000634 (2010)

MPG.PuRe

144.

Journal Article

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), pp. 10246 - 10254 (2010)

MPG.PuRe

145.

Journal Article

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), pp. F224 - F230 (2010)

MPG.PuRe

146.

Journal Article

Hub, J. S.; de Groot, B. L.: Detection of functional modes in protein dynamics. PLoS Computational Biology 5 (8), e1000480 (2009)

MPG.PuRe

147.

Journal Article

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), pp. 599 - 608 (2009)

MPG.PuRe

148.

Journal Article

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), pp. 30 - 46 (2009)

MPG.PuRe

149.

Journal Article

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), pp. 5207 - 5210 (2009)

MPG.PuRe

150.

Journal Article

Seeliger, D.; de Groot, B. L.: tCONCOORD-GUI: Visually supported conformational sampling of bioactive molecules. Journal of Computational Chemistry 30 (7), pp. 1160 - 1166 (2009)

MPG.PuRe