Publications of the Department (MPG.PuRe list)

299.

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

300.

Journal Article

Beissner, M.; Dutertre, S.; Schemm, R.; Danker, T.; Sporning, A.; Grubmüller, H.; Nicke, A.: Efficient binding of 4/7 α-conotoxins to nicotinic α4β2 receptors is prevented by Arg185 and Pro195 in the α4 subunit. Molecular Pharmacology 82 (4), pp. 711 - 718 (2012)

MPG.PuRe

301.

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

302.

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

303.

Journal Article

Sieben, C.; Kappel, C.; Zhu, R.; Wozniak, A.; Rankl, C.; Hinterdorfer, P.; Grubmüller, H.; Herrmann, A.: Influenza virus binds its host cell using multiple dynamic interactions. Proceedings of the National Academy of Sciences of the United States of America 106 (34), pp. 13626 - 13631 (2012)

MPG.PuRe

304.

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

305.

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

306.

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

307.

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

308.

Journal Article

Risselada, H. J.; Marelli, G.; Fuhrmans, M.; Smirnova, Y. G.; Grubmüller, H.; Marrink, S. J.; Müller , M.: Line-tension controlled mechanism for influenza fusion. PLoS One 7 (6), e38302 (2012)

MPG.PuRe

309.

Journal Article

Hensen, U.; Meyer, T.; Haas, J.; Rex, R.; Vriend, G.; Grubmüller, H.: Exploring protein dynamics space: The dynasome as the missing link between protein structure and function. PLoS One 7 (5), e33931 (2012)

MPG.PuRe

310.

Journal Article

Pool, R.; Heringa, J.; Höfling, M.; Schulz, R.; Smith, J. C.; Feenstra, K. A.: Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module. Journal of Computational Chemistry 33 (12), pp. 1207 - 1214 (2012)

MPG.PuRe

311.

Journal Article

Risselada, H. J.; Grubmuller, H.: How SNARE molecules mediate membrane fusion: Recent insights from molecular simulations. Current Opinion in Structural Biology 22 (2), pp. 187 - 196 (2012)

MPG.PuRe

312.

Journal Article

Znidarsic, A.; Godec, A.; Gaberscek , M.: pH-based one pot synthesis of biocompatible olive shaped inorganic particles. Materials Research Bulletin 47 (4), pp. 967 - 973 (2012)

MPG.PuRe

313.

Journal Article

Buelens, F. P.; Grubmüller, H.: Linear-scaling soft-core scheme for alchemical free energy calculations. Journal of Computational Chemistry 33 (1), pp. 25 - 33 (2012)

MPG.PuRe

314.

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

315.

Journal Article

Boggio-Pasqua, M.; Burmeister, C.; Robb, M. A.; Groenhof, G.: Photochemical reactions in biological systems: probing the effect of the environment by means of hybrid quantum chemistry/molecular mechanics simulations. Physical Chemistry Chemical Physics 14 (22), pp. 7912 - 7928 (2012)

MPG.PuRe

316.

Journal Article

Inhester, L.; Burmeister, C.; Groenhof, G.; Grubmuller, H.: Auger spectrum of a water molecule after single and double core ionization. Journal of Chemical Physics 136 (14), 144304 (2012)

MPG.PuRe

317.

Journal Article

Kappel, C.; Doelker, N.; Kumar , R.; Grubmüller, H.: Universal relaxation governs the nonequilibrium elasticity of biomolecules. Physical Review Letters 109 (11), 118304 (2012)

MPG.PuRe

318.

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

319.

Journal Article

Seeliger, D.; Soeroes, S.; Klingberg, R.; Schwarzer, D.; Grubmüller, H.; Fischle, W.: Quantitative assessment of protein interaction with methyl-lysine analogues by hybrid computational and experimental approaches. ACS Chemical Biology 7 (1), pp. 150 - 154 (2012)

MPG.PuRe

320.

Journal Article

Ukmar, T.; Maver, U.; Planinsek, O.; Pintar, A.; Kaucic, V.; Godec, A.; Gaberscek, M.: Guest-host van der Waals interactions decisively affect the molecular transport in mesoporous media. Journal of Materials Chemistry 22 (3), pp. 1112 - 1120 (2012)

MPG.PuRe

321.

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

322.

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

323.

Journal Article

Godec, A.; Smith, J. C.; Merzel, F.: Increase of both order and disorder in the first hydration shell with increasing solute polarity. Physical Review Letters 107 (26), 267801 (2011)

MPG.PuRe

324.

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

325.

Journal Article

Lopez, M.; Vu, H.; Wang, C. K.; Wolf, M. G.; Groenhof, G.; Innocenti, A.; Supuran, C. T.; Poulsen, S. A.: Promiscuity of carbonic anhydrase II. Unexpected ester hydrolysis of carbohydrate-based sulfamate inhibitors. Journal of the American Chemical Society 133 (45), pp. 18452 - 18462 (2011)

MPG.PuRe

326.

Journal Article

Ukmar, T.; Maver, U.; Planinsek, O.; Kaucic, V.; Gaberscek, M.; Godec, A.: Understanding controlled drug release from mesoporous silicates: Theory and experiment. Journal of Controlled Release 155 (3), pp. 409 - 417 (2011)

MPG.PuRe

327.

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

328.

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

329.

Journal Article

de Jong, D. H.; Schaefer, L. V.; de Vries, A. H.; Marrink, S. J.; Berendsen, H. J. C.; Grubmüller, H.: Determining equilibrium constants for dimerization reactions from molecular dynamics simulations. Journal of Computational Chemistry 32 (9), pp. 1919 - 1928 (2011)

MPG.PuRe

330.

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

331.

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

332.

Journal Article

Boggio-Pasqua, M.; Groenhof, G.: Controlling the photoreactivity of the photoactive yellow protein chromophore by substituting at the p-coumaric acid group. The Journal of Physical Chemistry B 115 (21), pp. 7021 - 7028 (2011)

MPG.PuRe

333.

Journal Article

Donnini, S.; Tegeler, F.; Groenhof, G.; Grubmüller, H.: Constant pH molecular dynamics in explicit solvent with lambda-dynamics. Journal of Chemical Theory and Computation 7 (6), pp. 1962 - 1978 (2011)

MPG.PuRe

334.

Journal Article

van den Bogaart, G.; Thutupalli, S.; Risselada, H. J.; Meyenberg, K.; Holt, M.; Riedel, D.; Diederichsen, U.; Herminghaus, S.; Grubmüller, H.; Jahn, R.: Synaptotagmin-1 may be a distance regulator acting upstream of SNARE nucleation. Nature Structural and Molecular Biology 18 (7), pp. 805 - 812 (2011)

MPG.PuRe

335.

Journal Article

Höfling, M.; Lima, N.; Haenni, D.; Seidel, C. A. M.; Schuler, B.; Grubmüller, H.: Structural heterogeneity and quantitative FRET efficiency distributions of polyprolines through a hybrid atomistic simulation and Monte Carlo approach. PLoS One 6 (5), e19791 (2011)

MPG.PuRe

336.

Journal Article

Czub, J.; Grubmüller, H.: Torsional elasticity and energetics of F-1-ATPase. Proceedings of the National Academy of Sciences of the United States of America 108 (18), pp. 7408 - 7413 (2011)

MPG.PuRe

337.

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

338.

Journal Article

Kutzner, C.; Czub, J.; Grubmüller, H.: Keep it flexible: Driving macromolecular rotary motions in atomistic simulations with GROMACS. Journal of Chemical Theory and Computation 7 (5), pp. 1381 - 1393 (2011)

MPG.PuRe

339.

Journal Article

Risselada, H. J.; Kutzner, C.; Grubmüller, H.: Caught in the act: Visualization of SNARE-mediated fusion events in molecular detail. Chembiochem 12 (7), pp. 1049 - 1055 (2011)

MPG.PuRe

340.

Journal Article

Risselada, H. J.; Marrink, S. J.; Mueller, M.: Curvature-dependent elastic properties of liquid-ordered domains result in inverted domain sorting on uniaxially compressed vesicles. Pysical Review Letters 106 (14), 148102 (2011)

MPG.PuRe

341.

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

342.

Journal Article

Kappel, C.; Grubmüller, H.: Velocity-dependent mechanical unfolding of bacteriorhodopsin is governed by a dynamic interaction network. Biophysical Journal 100 (4), pp. 1109 - 1119 (2011)

MPG.PuRe

343.

Journal Article

Godec, A.; Ukmar, T.; Gaberscek, M.; Merzel, F.: Inversion of pore size dependence of solute transport kinetics from increasingly attractive ordered porous matrix. Europhysics Letters 92 (6), 60011 (2011)

MPG.PuRe

344.

Journal Article

Ukmar, T.; Gaberscek, M.; Merzel, F.; Godec, A.: Modus operandi of controlled release from mesoporous matrices: A theoretical perspective. Physical Chemistry Chemical Physics 13 (3), pp. 15311 - 15317 (2011)

MPG.PuRe

345.

Journal Article

Ukmar, T.; Godec, A.; Planinsek, O.; Kaucic, V.; Mali, G.; Gaberscek, M.: The phase (trans)formation and physical state of a model drug in mesoscopic confinement. Physical Chemistry Chemical Physics 13 (35), pp. 16046 - 16054 (2011)

MPG.PuRe

346.

Journal Article

van den Bogaart, G.; Meyenberg, K.; Risselada, H. J.; Amin, H.; Willig, K.; Hubrich, B. E.; Dier, M.; Hell, S. W.; Grubmüller, H.; Diederichsen, U. et al.; Jahn, R.: Membrane protein sequestering by ionic protein–lipid interactions. Nature 479 (7374), doi:10.1038/nature10545, pp. 552 - 555 (2011)

MPG.PuRe

347.

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

348.

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

349.

Journal Article

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)

MPG.PuRe

350.

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

351.

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

352.

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

353.

Journal Article

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)

MPG.PuRe

354.

Journal Article

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)

MPG.PuRe

355.

Journal Article

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)

MPG.PuRe

356.

Journal Article

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)

MPG.PuRe

357.

Journal Article

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)

MPG.PuRe

358.

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

359.

Journal Article

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)

MPG.PuRe

360.

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

361.

Journal Article

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)

MPG.PuRe

362.

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

363.

Journal Article

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)

MPG.PuRe

364.

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

365.

Journal Article

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)

MPG.PuRe

366.

Journal Article

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)

MPG.PuRe

367.

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

368.

Journal Article

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

MPG.PuRe

369.

Journal Article

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)

MPG.PuRe

370.

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

371.

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

372.

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

373.

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

374.

Journal Article

Kim, S.; Gailite, I.; Moussian, B.; Luschnig, S.; Goette, M.; Fricke, K.; Honemann-Capito, M.; Grubmuller, H.; Wodarz, A.: Kinase-activity-independent functions of atypical protein kinase C in Drosophila. Journal of Cell Science 122, pp. 3759 - 3771 (2009)

MPG.PuRe

375.

Journal Article

Boggio-Pasqua, M.; Robb, M. A.; Groenhof, G.: Hydrogen bonding controls excited-state decay of the photoactive yellow protein chromophore. Journal of the American Chemical Society 131 (38), pp. 13580 - 13581 (2009)

MPG.PuRe

376.

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

377.

Journal Article

Goette, M.; Stumpe, M. C.; Ficner, R.; Grubmueller, H.: Molecular determinants of snurportin 1 ligand affinity and structural response upon binding. Biophysical Journal 97 (2), pp. 581 - 589 (2009)

MPG.PuRe

378.

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

379.

Journal Article

Haas, J.; Vöhringer-Martinez, E.; Bögehold, A.; Matthes, D.; Hensen, U.; Pelah, A.; Abel, B.; Grubmuller, H.: Primary steps of pH-dependent insulin aggregation kinetics are governed by conformational flexibility. ChemBioChem 10 (11), pp. 1816 - 1822 (2009)

MPG.PuRe

380.

Journal Article

Donnini, S.; Villa, A.; Groenhof, G.; Mark, A. E.; Wierenga, R. K.; Juffer, A. H.: Inclusion of ionization states of ligands in affinity calculations. Proteins: Structure, Function, and Bioinformatics 76 (1), pp. 138 - 150 (2009)

MPG.PuRe

381.

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

382.

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

383.

Journal Article

Stumpe, M. C.; Grubmuller, H.: Urea impedes the hydrophobic collapse of partially unfolded proteins. Biophysical Journal 96 (9), pp. 3744 - 3752 (2009)

MPG.PuRe

384.

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

385.

Journal Article

Reinhard, F.; Lange, O.F.; Hub, J.S.; Haas, J.; Grubmüller, H.: g_permute: Permutation-reduced phase space density compaction. Computer Physics Communications 180 (3), pp. 455 - 458 (2009)

MPG.PuRe

386.

Journal Article

Zink, M.; Grubmuller, H.: Mechanical properties of the icosahedral shell of southern bean mosaic virus: a molecular dynamics study. Biophysical Journal 96 (4), pp. 1350 - 1363 (2009)

MPG.PuRe

387.

Journal Article

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

MPG.PuRe

388.

Journal Article

Goette, M.; Grubmuller, H.: Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes. Journal of Computational Chemistry 30 (3), pp. 447 - 456 (2009)

MPG.PuRe

389.

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)

MPG.PuRe

390.

Journal Article

Godec, A.; Gaberscek, M.; Jamnik , J.; Merzel, F.: Nonlinear diffusion in two-dimensional ordered porous media based on a free volume theory. The Journal of Chemical Physics 131 (23), 234106 (2009)

MPG.PuRe

391.

Journal Article

Godec, A.; Gaberscek, M.; Jamnik, J.: Comment on the article “A new understanding of the relationship between solubility and particle size” by W. Wu and G.H. Nancollas. Journal of Solution Chemistry 38 (1), pp. 135 - 146 (2009)

MPG.PuRe

392.

Journal Article

Hensen, U.; Grubmüller, H.; Lange, O. F.: Adaptive anisotropic kernels for nonparametric estimation of absolute configurational entropies in high-dimensional configuration spaces. Physical Review E 80 (1), 011913 (2009)

MPG.PuRe

393.

Journal Article

Link, O.; Voehringer-Martinez, E.; Lugovoi, E.; Liu, Y.; Siefermann, K.; Faubel, M.; Grubmuller, H.; Gerber, R. B.; Miller, Y.; Abel, B.: Ultrafast phase transitions in metastable water near liquid interfaces. Faraday Discussions 141, DOI: 10.1039/b811659h, pp. 67 - 79 (2009)

MPG.PuRe

394.

Journal Article

Ukmar, T.; Godec, A.; Maver, U.; Planinsek, O.; Bele, M.; Jamnik, J.; Gaberscek, M.: Suspensions of modified TiO2 nanoparticles with supreme UV filtering ability. Journal of Materials Chemistry 19 (43), pp. 8176 - 8183 (2009)

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