Publications of the Department (MPG.PuRe list)

Journal Article (26)

1.
Journal Article
Smirnova, Y. G.; Aeffner, S.; Risselada, H. J.; Salditt, T.; Marrink, S. J.; Müller, M.; Knecht, V.: Interbilayer repulsion forces between tension-free lipid bilayers from simulation. Soft Matter 9 (45), pp. 10705 - 10718 (2013)
2.
Journal Article
Xiang, S. Q.; Gapsys, V.; Kim, H. Y.; Bessonov, S.; Hsiao, H. H.; Möhlmann, S.; Klaukien, V.; Ficner, R.; Becker, S.; Urlaub, H. et al.; Lührmann, R.; de Groot, B.; Zweckstetter, M.: Phosphorylation drives a dynamic switch in serine/arginine-rich proteins. Structure 21 (12), pp. 2162 - 2174 (2013)
3.
Journal Article
Blau, C.; Grubmüller, H.: g_contacts: Fast contact search in bio-molecular ensemble data. Computer Physics Communications 184 (12), pp. 2856 - 2859 (2013)
4.
Journal Article
Bock, L. V.; Blau, C.; Schröder, G. F.; Davydov, I. I.; Fischer, N.; Stark, H.; Rodnina, M. V.; Vaiana, A. C.; Grubmüller, H.: Energy barriers and driving forces in tRNA translocation through the ribosome. Nature Structural and Molecular Biology 20 (12), pp. 1390 - 1396 (2013)
5.
Journal Article
Gapsys, V.; de Groot, B. L.; Briones, R.: Computational analysis of local membrane properties. Journal of Computer-Aided Molecular Design 27 (10), pp. 845 - 858 (2013)
6.
Journal Article
Paltrinieri, L.; Borsari, M.; Battistuzzi, G.; Sola, M.; Dennison, C.; de Groot, B. L.; Corni, S.; Bortolotti, C. A.: How the dynamics of the metal-binding loop region controls the acid transition in cupredoxins. Biochemistry 52 (42), pp. 7397 - 7404 (2013)
7.
Journal Article
Vesper, M. D.; de Groot, B. L.: Collective dynamics underlying allosteric transitions in hemoglobin. PLoS Computational Biology 9 (9), e1003232 (2013)
8.
Journal Article
Bennett, W. F. D.; Chen, A. W.; Donnini, S.; Groenhof, G.; Tieleman, D. P.: Constant pH simulations with the coarse-grained MARTINI model—Application to oleic acid aggregates. Canadian Journal of Chemistry 91 (9), pp. 839 - 846 (2013)
9.
Journal Article
Godec, A.; Smith, J. C.; Merzel, F.: Soft collective fluctuations governing hydrophobic association. Physical Review Letters 111 (12-20), 127801 (2013)
10.
Journal Article
Li, W.; Edwards, S. A.; Lu, L.; Kubar, T.; Patil, S. P.; Grubmüller, H.; Groenhof, G.; Gräter, F.: Force distribution analysis of mechanochemically reactive dimethylcyclobutene. ChemPhysChem 14 (12), pp. 2687 - 2697 (2013)
11.
Journal Article
Doelker, N.; Blanchet, C. E.; Voss, B.; Haselbach, D.; Kappel, C.; Monecke, T.; Svergun, D. I.; Stark, H.; Ficner, R.; Zachariae, U. et al.; Grubmüller, H.; Dickmanns, A.: Structural determinants and mechanism of mammalian CRM1 allostery. Structure 21 (8), pp. 1350 - 1360 (2013)
12.
Journal Article
Godec, A.; Metzler, R.: Linear response, fluctuation-dissipation, and finite-system-size effects in superdiffusion. Physical Review E 88 (1), 012116 (2013)
13.
Journal Article
Assentoft, M.; Kaptan, S.; Fenton, R. A.; Hua, S. Z.; de Groot, B. L.; MacAulay, N.: Phosphorylation of rat aquaporin-4 at Ser111 is not required for channel gating. Glia 61 (7), pp. 1101 - 1112 (2013)
14.
Journal Article
Meyer, T.; Gabelica, V.; Grubmüller, H.; Orozco, M.: Proteins in the gas phase. Wiley Interdisciplinary Reviews: Computational Molecular Science 3 (4), pp. 408 - 425 (2013)
15.
Journal Article
Brandani, G. B.; Schor, M.; MacPhee, C. E.; Grubmüller, H.; Zachariae, U.; Marenduzzo, D.: Quantifying disorder through conditional entropy: An application to fluid mixing. PLoS One 8 (6), e65617 (2013)
16.
Journal Article
Lindner, T.; de Groot, B. L.; Stary-Weinzinger, A.: Probing the energy landscape of activation gating of the bacterial potassium channel KcsA. PLoS Computational Biology 9 (5), e1003058 (2013)
17.
Journal Article
Wacker, S.; Aponte-Santamaria, C. A.; Kjellbom, P.; Nielsen, S.; de Groot, B. L.; Rützler, M.: The identification of novel, high affinity AQP9 inhibitors in an intracellular binding site. Molecular Membrane Biology 30 (3), pp. 246 - 260 (2013)
18.
Journal Article
Inhester, L.; Groenhof, G.; Grubmüller, H.: Core hole screening and decay rates of double core ionized first row hydrides. The Journal of Chemical Physics 138 (16), 164304 (2013)
19.
Journal Article
Vukovic, L.; Burmeister, C. F.; Kral, P.; Groenhof, G.: Control mechanisms of photoisomerization in protonated Schiff bases. The Journal of Physical Chemistry Letters 4 (6), pp. 1005 - 1011 (2013)
20.
Journal Article
Song, C.; Weichbrodt, C.; Salnikov, E.; Dynowski, M.; Forsberg, B.; Bechinger, B.; Steinem, C.; de Groot, B. L.; Zachariae, U.; Zeth, K.: Crystal structure and functional mechanism of a human antimicrobial membrane channel. Proceedings of the National Academy of Sciences of the United States of America 110 (12), pp. 4586 - 4591 (2013)
21.
Journal Article
Seeliger, D.; Zapater, C.; Krenc, D.; Haddoub, R.; Flitsch, S.; Beitz, E.; Cerdà, J.; De Groot, B. L.: Discovery of novel human aquaporin-1 blockers. ACS Chemical Biology 8 (1), pp. 249 - 256 (2013)
22.
Journal Article
Monecke, T.; Haselbach, D.; Voß, D.; Russek, A.; Neumann, P.; Thomson, E.; Hurt, E.; Zachariae, U.; Stark, H.; Grubmüller, H. et al.; Dickmanns, A.; Ficner, R.: Structural basis for cooperativity of CRM1 export complex formation. Proceedings of the National Academy of Sciences of the United States of America 110 (3), pp. 960 - 965 (2013)
23.
Journal Article
Godec, A.; Metzler, R.: Finite-time effects and ultraweak ergodicity breaking in superdiffusive dynamics. Physical Review Letters 110 (2), 020603 (2013)
24.
Journal Article
Gapsys, V.; de Groot, B. L.: Optimal superpositioning of flexible molecule ensemble. Biophysical Journal 104 (1), pp. 196 - 207 (2013)
25.
Journal Article
Hoefling, M.; Grubmüller, H.: In silico FRET from simulated dye dynamics. Computer physics communications 184 (3), pp. 841 - 852 (2013)
26.
Journal Article
Honigmann, A.; van den Bogaart, G.; Iraheta, E.; Risselada, H. J.; Milovanovic, D.; Müller, V.; Müller, S.; Diederichsen, U.; Fasshauer, D.; Grubmüller, H. et al.; Hell, S. W.; Eggeling, C.; Kühnel, K.; Jahn, R.: Phosphatidylinositol 4,5-bisphosphate clusters act as molecular beacons for vesicle recruitment. Nature Structural and Molecular Biology 20, pp. 679 - 686 (2013)

Book Chapter (1)

27.
Book Chapter
Groenhof, G.: Introduction to QM/MM simulations. In: Biomolecular Simulations: Mehods and Protocols, pp. 43 - 66 (Eds. Monticelli, L.; Salonen, E.). Humana Pr.; Springer, New York (2013)
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