Publications of the Department (MPG.PuRe list)

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)

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)

Maver, U.; Znidarsic, A.; Saboti, D.; Srcic, S.; Gaberscek, M.; Godec, A.; Planinsek , O.: The relation between the interfacial contact and SiO₂ coating efficiency and properties in the case of two clarithromycin polymorphs. Colloids and Surfaces A: Physicochemical and Engineering Aspects 371 (1-3), pp. 119 - 125 (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)

Godec, A.; Gaberscek, M.; Jamnik , J.; Janezic, D.; Merzel, F.: Ion-size effect within the aqueous solution interface at the Pt(111) surface: Molecular dynamics studies. Physical Chemistry Chemical Physics 12 (41), pp. 13566 - 13573 (2010)

Forwood, J. K.; Lange, A.; Zachariae, U.; Marfori, M.; Preast, C.; Grubmüller, H.; Stewart, M.; Corbett, A. H.; Kobe, B.: Quantitative structural analysis of importin-β flexibility: Paradigm for solenoid protein structures. Structure 18 (9), pp. 1171 - 1183 (2010)

Kappel, C.; Zachariae, U.; Dölker, N.; Grubmüller, H.: An unusual hydrophobic core confers extreme flexibility to HEAT repeat proteins. Biophysical Journal 99 (5), pp. 1596 - 1603 (2010)

Bock, L. V.; Hutchings, B.; Grubmueller, H.; Woodbury, D. J.: Chemomechanical regulation of SNARE proteins studied with molecular dynamics simulations. Biophysical Journal 99 (4), pp. 1221 - 1230 (2010)

Wolf, M. G.; Hoefling, M.; Aponte-Santamaria, C.; Grubmueller, H.; Groenhof, G.: g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation. Journal of Computational Chemistry 31 (11), pp. 2169 - 2174 (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)

Dölker, N.; Zachariae, U.; Grubmüller, H.: Hydrophilic linkers and polar contacts affect aggregation of FG repeat peptides. Biophysical Journal 98 (11), pp. 2653 - 2661 (2010)

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

Brakemann, T.; Weber, G.; Andresen, M.; Groenhof, G.; Stiel, A. C.; Trowitzsch, S.; Eggeling, C.; Grubmueller, H.; Hell, S. W.; Wahl, M. et al.; Jakobs, S.: Molecular basis of the light-driven switching of the photochromic fluorescent protein padron. Journal of Biological Chemistry 285 (19), pp. 14603 - 14609 (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)

Nunes, J. M.; Hensen, U.; Ge, L.; Lipinsky, M.; Helenius, J.; Grubmueller, H.; Mueller, D. J.: A “Force Buffer” protecting immunoglobulin titin. Angewandte Chemie International Edition 49 (20), pp. 3528 - 3531 (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)

Woehri, A.; Katona, G.; Johansson, L. C.; Fritz, E.; Malmerberg, E.; Andersson, M.; Vincent, J.; Eklund, M.; Cammarata, M.; Wulff, M. et al.; Davidsson, J.; Groenhof, G.; Neutze, R.: Light-induced structural changes in a photosynthetic reaction center caught by Laue diffraction. Science 328 (5978), pp. 630 - 633 (2010)

Planinsek, O.; Zadnik, J.; Kunaver, M.; Srcic, S.; Godec, A.: Structural evolution of indomethacin particles upon milling: Time-resolved quantification and localization of disordered structure studied by IGC and DSC. Journal of Pharmaceutical Sciences 99 (4), pp. 1968 - 1981 (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)

Hensen, U.; Lange, O.; Grubmueller, H.: Estimating absolute configurational entropies of macromolecules: The minimally coupled subspace approach. PLoS ONE 5 (2), e9179 (2010)

Zink, M.; Grubmueller, H.: Primary changes of the mechanical properties of Southern Bean Mosaic Virus upon calcium removal. Biophysical Journal 98 (4), pp. 687 - 695 (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)

Groenhof, G.; Boggio-Pasqua, M.; Schäfer, L. V.; Robb, M. A.: Computer simulations of photobiological processes: The effect of the protein environment. In: Combining quantum mechanics and molecular mechanics. Some recent progresses in QM/MM methods, pp. 181 - 212 (Eds. Sabin, J. R.; Braendas, E.; Canuto, S.). Elsevier, Amsterdam (2010)