Publications

151.

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)

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152.

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)

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153.

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)

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154.

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)

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155.

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)

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156.

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)

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157.

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)

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158.

Journal Article

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

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159.

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)

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supplementary-material

160.

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)

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161.

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

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162.

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)

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163.

Journal Article

Portella, G.; de Groot, B. L.: Determinants of water permeability through nanoscopic hydrophilic channels. Biophysical Journal 96 (3), pp. 925 - 938 (2009)

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supplementary-material

164.

Journal Article

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), pp. 3 - 4 (2009)

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165.

Journal Article

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), pp. 1433 - 1437 (2008)

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166.

Journal Article

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), pp. 1175 - 1182 (2008)

MPG.PuRe

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167.

Journal Article

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), pp. 139 - 155 (2008)

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DOI

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supplementary-material

168.

Journal Article

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), pp. 1471 - 1475 (2008)

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supplementary-material

169.

Journal Article

Zachariae, U.; Grubmueller, H.: Importin-β: structural and dynamic determinants of a molecular spring. Structure 16 (6), pp. 906 - 915 (2008)

MPG.PuRe

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170.

Journal Article

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), pp. 747 - 754 (2008)

MPG.PuRe

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171.

Journal Article

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), pp. 352 - 363 (2008)

MPG.PuRe

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172.

Journal Article

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), pp. 1198 - 1203 (2008)

MPG.PuRe

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173.

Journal Article

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, pp. 1837 - 1850 (2008)

MPG.PuRe

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174.

Journal Article

Mueller, E. M.; Hub, J.; Grubmueller, H.; de Groot, B. L.: Is TEA an inhibitor for human Aquaporin-1? Pfluegers Archiv 456 (4), pp. 663 - 669 (2008)

MPG.PuRe

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175.

Journal Article

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, pp. 2275 - 2282 (2008)

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176.

Journal Article

Seeliger, D.; Haas, J.; de Groot, B. L.: Geometry-based sampling of conformational transitions in proteins. Structure 15 (11), pp. 1482 - 1492 (2007)

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177.

Journal Article

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), pp. 3156 - 3168 (2007)

MPG.PuRe

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178.

Journal Article

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), pp. 919 - 931 (2007)

MPG.PuRe

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179.

Journal Article

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), pp. 595 - 601 (2007)

MPG.PuRe

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180.

Journal Article

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), pp. 3930 - 3937 (2007)

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181.

Journal Article

Kubitzki, M. B.; de Groot, B. L.: Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange. Biophysical Journal 92, pp. 4262 - 4270 (2007)

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182.

Journal Article

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), pp. 2075 - 2084 (2007)

MPG.PuRe

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183.

Journal Article

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), pp. 831 - 846 (2006)

MPG.PuRe

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184.

Journal Article

Graeter, F.; de Groot, B. L.; Jiang, H.; Grubmueller, H.: Ligand-release pathways in the pheromone-binding protein of Bombyx mori. Structure 14 (10), pp. 1567 - 1576 (2006)

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185.

Journal Article

Zachariae, U.; Grubmueller, H.: A highly strained nuclear conformation of the exportin Cse1p revealed by molecular dynamics simulations. Structure 14 (9), pp. 1469 - 1478 (2006)

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186.

Journal Article

Hub, J. S.; de Groot, B. L.: Does CO2 permeate through Aquaporin-1? Biophysical Journal 91 (3), pp. 842 - 848 (2006)

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187.

Journal Article

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), pp. 14207 - 14214 (2006)

MPG.PuRe

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188.

Journal Article

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), pp. 1165 - 1178 (2006)

MPG.PuRe

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189.

Journal Article

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), pp. 1165 - 1178 (2006)

MPG.PuRe

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190.

Journal Article

de Groot, B. L.; Boeckmann, R. A.; Grubmueller, H.: Proteindynamik-Simulationen. Molekulare Nanomaschinen unter der Lupe. Physik in unserer Zeit 37, pp. 73 - 79 (2006)

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supplementary-material

191.

Journal Article

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)

MPG.PuRe

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192.

Journal Article

Seeliger, D.; de Groot, B. L.: Prediction of protein flexibility from geometrical constraints. Bio Tech Interantional 18, pp. 20 - 22 (2006)

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193.

Journal Article

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, pp. 955 - 966 (2006)

MPG.PuRe

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194.

Journal Article

Zachariae, U.; Grubmüller, H.: Prediction of a RanGTP-induced conformational switch in the exportin CAS/Cse1p by molecular dynamics simulations. MPIbpc News 5, pp. 1 - 6 (2006)

MPG.PuRe

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195.

Journal Article

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), pp. 5675 - 5685 (2005)

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196.

Journal Article

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), pp. 2113 - 2120 (2005)

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197.

Journal Article

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), pp. 611 - 616 (2005)

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198.

Journal Article

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), pp. 278 - 289 (2005)

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DOI

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199.

Journal Article

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), pp. 176 - 183 (2005)

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200.

Journal Article

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), pp. 3394 - 3399 (2005)

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Journal Article (201)