Publications of the Department (MPG.PuRe list)

Journal Article (22)

1.
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)
2.
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)
3.
Journal Article
Hub, J. S.; de Groot, B. L.: Detection of functional modes in protein dynamics. PLoS Computational Biology 5 (8), e1000480 (2009)
4.
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)
5.
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)
6.
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)
7.
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)
8.
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)
9.
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)
10.
Journal Article
Stumpe, M. C.; Grubmuller, H.: Urea impedes the hydrophobic collapse of partially unfolded proteins. Biophysical Journal 96 (9), pp. 3744 - 3752 (2009)
11.
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)
12.
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)
13.
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)
14.
Journal Article
Portella, G.; de Groot, B. L.: Determinants of water permeability through nanoscopic hydrophilic channels. Biophysical Journal 96 (3), pp. 925 - 938 (2009)
15.
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)
16.
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)
17.
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)
18.
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)
19.
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)
20.
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)
21.
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)
22.
Journal Article
Zink, M.; Grubmuller, H.: Simulation of a complete viral shell. Innovatives Supercomputing in Deutschland 7 (2), pp. 22 - 25 (2009)

Book Chapter (3)

23.
Book Chapter
Groenhof, G.; Schaefer, L. V.; Boggio-Pasqua, M.; Robb, M. A.: Excited state dynamics in biomolecules. In: Handbook of molecular biophysics, pp. 93 - 128 (Ed. Bohr, H. G.). Wiley-VCH, Weinheim (2009)
24.
Book Chapter
Hub, J.; Grubmuller, H.; de Groot, B. L.: Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations? In: Aquaporins, pp. 57 - 76 (Ed. Beitz, E.). Springer, Berlin (2009)
25.
Book Chapter
Kubitzki, M. B.; de Groot, B. L.; Seeliger, D.: Protein dynamics: From structure to function. In: From Protein Structure to Function with Bioinformatics, pp. 217 - 249 (Ed. Rigden, D.J.). Springer, Dordrecht (2009)
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