Publikationen der Abteilung für Theoretische Biophysik (TB)

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Zeitschriftenartikel (19)

1.
Zeitschriftenartikel
Gecht, M.; Siggel, M.; Linke, M.; Hummer, G.; Köfinger, J.: MDBenchmark: A toolkit to optimize the performance of molecular dynamics simulations. The Journal of Chemical Physics 153 (14), 144105 (2020)
2.
Zeitschriftenartikel
Jost Lopez, A.; Quoika, P. K.; Linke, M.; Hummer, G.; Köfinger, J.: Quantifying Protein-Protein Interactions in Molecular Simulations. The Journal of Physical Chemistry B 124 (23), S. 4673 - 4685 (2020)
3.
Zeitschriftenartikel
Linker, S. M.; Magarkar, A.; Köfinger, J.; Hummer, G.; Seeliger, D.: Fragment Binding Pose Predictions Using Unbiased Simulations and Markov-State Models. Journal of Chemical Theory and Computation 15 (9), S. 4974 - 4981 (2019)
4.
Zeitschriftenartikel
Vögele, M.; Köfinger, J.; Hummer, G.: Finite-Size-Corrected Rotational Diffusion Coefficients of Membrane Proteins and Carbon Nanotubes from Molecular Dynamics Simulations. The Journal of Physical Chemistry B 123 (24), S. 5099 - 5106 (2019)
5.
Zeitschriftenartikel
Köfinger, J.; Stelzl, L. S.; Reuter, K.; Allande, C.; Reichel, K.; Hummer, G.: Efficient Ensemble Refinement by Reweighting. Journal of Chemical Theory and Computation 15 (5), S. 3390 - 3409 (2019)
6.
Zeitschriftenartikel
Reuter, K.; Köfinger, J.: CADISHI: Fast parallel calculation of particle-pair distance histograms on CPUs and GPUs. Computer Physics Communications 236, S. 274 - 284 (2019)
7.
Zeitschriftenartikel
Reichel, K.; Stelzl, L. S.; Köfinger, J.; Hummer, G.: Precision DEER Distances from Spin-Label Ensemble Refinement. The Journal of Physical Chemistry Letters 9 (18), S. 5748 - 5752 (2018)
8.
Zeitschriftenartikel
Vögele, M.; Köfinger, J.; Hummer, G.: Molecular dynamics simulations of carbon nanotube porins in lipid bilayers. Faraday Discussions 209, S. 341 - 358 (2018)
9.
Zeitschriftenartikel
Vögele, M.; Köfinger, J.; Hummer, G.: Hydrodynamics of Diffusion in Lipid Membrane Simulations. Physical Review Letters 120 (26), 268104 (2018)
10.
Zeitschriftenartikel
Linke, M.; Köfinger, J.; Hummer, G.: Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations. The Journal of Physical Chemistry Letters 9 (11), S. 2874 - 2878 (2018)
11.
Zeitschriftenartikel
Linke, M.; Köfinger, J.; Hummer, G.: Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations. The Journal of Physical Chemistry B 122 (21), S. 5630 - 5639 (2018)
12.
Zeitschriftenartikel
Bhaskara, R.; Linker, S. M.; Vögele, M.; Köfinger, J.; Hummer, G.: Carbon Nanotubes Mediate Fusion of Lipid Vesicles. ACS Nano 11 (2), S. 1273 - 1280 (2017)
13.
Zeitschriftenartikel
Hummer, G.; Köfinger, J.: Bayesian ensemble refinement by replica simulations and reweighting. The Journal of Chemical Physics 143 (24), S. 243150-1 - 243150-14 (2015)
14.
Zeitschriftenartikel
Barends, T. R.M.; Foucar, L.; Ardevol, A.; Nass, K.; Aquila, A.; Botha, S.; Doak, R. B.; Falahati, K.; Hartmann, E.; Hilpert, M. et al.; Heinz, M.; Hoffmann, M. C.; Köfinger, J.; Koglin, J. E.; Kovacsova, G.; Liang, M.; Milathianaki, D.; Lemke, H. T.; Reinstein, J.; Roome, C. M.; Shoeman, R. L.; Williams, G. J.; Burghardt, I.; Hummer, G.; Boutet, S.; Schlichting, I.: Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation. Science 350 (6259), S. 445 - 450 (2015)
15.
Zeitschriftenartikel
Köfinger, J.; Ragusa, M. J.; Lee, I.-H.; Hummer, G.; Hurley, J. H.: Solution Structure of the Atg1 Complex: Implications for the Architecture of the Phagophore Assembly Site. Structure 23 (5), S. 809 - 818 (2015)
16.
Zeitschriftenartikel
Köfinger, J.; Hummer, G.: Atomic-resolution structural information from scattering experiments on macromolecules in solution. Physical Review E 87, 052712 (2013)
17.
Zeitschriftenartikel
Köfinger, J.; Hummer, G.; Dellago, C.: Single-file water in nanopores. Physical Chemistry Chemical Physics 13 (34), S. 15403 - 15417 (2011)
18.
Zeitschriftenartikel
Köfinger, J.; Hummer, G.; Dellago, C.: A one-dimensional dipole lattice model for water in narrow nanopores. The Journal of Chemical Physics 130 (15), 154110 (2009)
19.
Zeitschriftenartikel
Köfinger, J.; Hummer, G.; Dellago, C.: Macroscopically ordered water in nanopores. Proceedings of the National Academy of Sciences of the United States of America 105 (36), S. 13218 - 13222 (2008)

Buchkapitel (1)

20.
Buchkapitel
Köfinger, J.; Rózycki, B.; Hummer, G.: Inferring Structural Ensembles of Flexible and Dynamic Macromolecules Using Bayesian, Maximum Entropy, and Minimal-Ensemble Refinement Methods. In: Methods in Molecular Biology, Bd. 2022, S. 341 - 352. Springer (2019)
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