Publications of B. L. de Groot

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)

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)

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)

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)

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)

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

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)

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)

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)

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)

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

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)

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)

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

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)

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)

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)

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)

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

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)