Publications of the Department (MPG.PuRe list)

Wolf, M. G.; Groenhof, G.: Evaluating nonpolarizable nucleic acid force fields: A systematic comparison of the nucleobases hydration free energies and water-chloroform partition coefficients. Journal of Computational Chemistry 33 (28), pp. 2225 - 2232 (2012)

Godec, A.; Merzel, F.: Physical origin underlying the entropy loss upon hydrophobic hydration. Journal of the American Chemical Society 134 (42), pp. 17575 - 17581 (2012)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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

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)

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)

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)

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)