PD Dr. Jürgen Köfinger

PD Dr. Jürgen Köfinger

Project Leader

Jürgen Köfinger Publications

Journal Article (27)

2024
Journal Article
Köfinger, J.; Hummer, G.: Encoding prior knowledge in ensemble refinement. The Journal of Chemical Physics 160, 114111 (2024)
Journal Article
Vögele, M.; Köfinger, J.; Hummer, G.: Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly. ACS applied bio materials 7 (2), pp. 528 - 534 (2024)
2022
Journal Article
Linke, M.; Quoika, P. K.; Bramas, B.; Köfinger, J.; Hummer, G.: Complexes++: Efficient and versatile coarse-grained simulations of protein complexes and their dense solutions. The Journal of Chemical Physics 157 (20), 204802 (2022)
Journal Article
Siggel, M.; Kehl, S.; Reuter, K.; Köfinger, J.; Hummer, G.: TriMem: A parallelized hybrid Monte Carlo software for efficient simulations of lipid membranes. The Journal of Chemical Physics 157 (17), 174801 (2022)
Journal Article
Stelzl, L. S.; Pietrek, L. M.; Holla, A.; Oroz, J.; Sikora, M.; Köfinger, J.; Schuler, B.; Zweckstetter, M.; Hummer, G.: Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure. JACS Au 2 (3), pp. 673 - 686 (2022)
2021
Journal Article
Köfinger, J.; Hummer, G.: Empirical optimization of molecular simulation force fields by Bayesian inference. The European Physical Journal B: Condensend Matter Physics 94 (12), 245 (2021)
Journal Article
Klaus, M.; Rossini, E.; Linden, A.; Paithankar, K. S.; Zeug, M.; Ignatova, Z.; Urlaub, H.; Khosla, C.; Köfinger, J.; Hummer, G. et al.; Grininger, M.: Solution Structure and Conformational Flexibility of a Polyketide Synthase Module. JACS Au 1 (12), pp. 2162 - 2171 (2021)
Journal Article
Ho, N. T.; Siggel, M.; Camacho, K. V.; Bhaskara, R.; Hicks, J. M.; Yao, Y.-C.; Zhang, Y.; Köfinger, J.; Hummer, G.; Noy, A.: Membrane fusion and drug delivery with carbon nanotube porins. Proceedings of the National Academy of Sciences of the United States of America 118 (19), e2016974118 (2021)
2020
Journal Article
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)
Journal Article
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), pp. 4673 - 4685 (2020)
2019
Journal Article
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), pp. 4974 - 4981 (2019)
Journal Article
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), pp. 5099 - 5106 (2019)
Journal Article
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), pp. 3390 - 3409 (2019)
Journal Article
Reuter, K.; Köfinger, J.: CADISHI: Fast parallel calculation of particle-pair distance histograms on CPUs and GPUs. Computer Physics Communications 236, pp. 274 - 284 (2019)
2018
Journal Article
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), pp. 5748 - 5752 (2018)
Journal Article
Vögele, M.; Köfinger, J.; Hummer, G.: Molecular dynamics simulations of carbon nanotube porins in lipid bilayers. Faraday Discussions 209, pp. 341 - 358 (2018)
Journal Article
Vögele, M.; Köfinger, J.; Hummer, G.: Hydrodynamics of Diffusion in Lipid Membrane Simulations. Physical Review Letters 120 (26), 268104 (2018)
Journal Article
Linke, M.; Köfinger, J.; Hummer, G.: Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations. The Journal of Physical Chemistry Letters 9 (11), pp. 2874 - 2878 (2018)
Journal Article
Linke, M.; Köfinger, J.; Hummer, G.: Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations. The Journal of Physical Chemistry B 122 (21), pp. 5630 - 5639 (2018)
2017
Journal Article
Bhaskara, R.; Linker, S. M.; Vögele, M.; Köfinger, J.; Hummer, G.: Carbon Nanotubes Mediate Fusion of Lipid Vesicles. ACS Nano 11 (2), pp. 1273 - 1280 (2017)
2015
Journal Article
Hummer, G.; Köfinger, J.: Bayesian ensemble refinement by replica simulations and reweighting. The Journal of Chemical Physics 143 (24), pp. 243150-1 - 243150-14 (2015)
Journal Article
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), pp. 445 - 450 (2015)
Journal Article
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), pp. 809 - 818 (2015)
2013
Journal Article
Köfinger, J.; Hummer, G.: Atomic-resolution structural information from scattering experiments on macromolecules in solution. Physical Review E 87, 052712 (2013)
2011
Journal Article
Köfinger, J.; Hummer, G.; Dellago, C.: Single-file water in nanopores. Physical Chemistry Chemical Physics 13 (34), pp. 15403 - 15417 (2011)
2009
Journal Article
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)
2008
Journal Article
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), pp. 13218 - 13222 (2008)

Book Chapter (1)

2019
Book Chapter
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, Vol. 2022, pp. 341 - 352. Springer (2019)

Thesis - Habilitation (1)

2022
Thesis - Habilitation
Köfinger, J.: Integrating Experiments and Molecular Simulations by Ensemble Refinement. Habilitation, 79 pp., Fachbereich Physik, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main (2022)
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