Gerhard Hummer: Theoretical Biophysics – Department Publications

Berman, H. M.; Adams, P. D.; Bonvin, A. A.; Burley, S. K.; Carragher, B.; Chiu, W.; DiMaio, F.; Ferrin, T. E.; Gabanyi, M. J.; Goddard, T. D. et al.; Griffin, P. R.; Haas, J.; Hanke, C. A.; Hoch, J. C.; Hummer, G.; Kurisu, G.; Lawson, C. L.; Leitner, A.; Markley, J. L.; Meiler, J.; Montelione, G. T.; Phillips, G. N.; Prisner, T.; Rappsilber, J.; Schriemer, D. C.; Schwede, T.; Seidel, C. A. M.; Strutzenberg, T. S.; Svergun, D. I.; Tajkhorshid, E.; Trewhella, J.; Vallat, B.; Velankar, S.; Vuister, G. W.; Webb, B.; Westbrook, J. D.; White, K. L.; Sali, A.: Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure 27 (12), pp. 1745 - 1759 (2019)

Baldering, T. N.; Bullerjahn, J. T.; Hummer, G.; Heilemann, M.; Malkusch, S.: Molecule counts in complex oligomers with single-molecule localization microscopy. Journal of Physics D: Applied Physics 52 (47), 474002 (2019)

Herhaus, L.; Bhaskara, R.; Lystad, A. H.; Gestal-Mato, U.; Covarrubias-Pinto, A.; Bonn, F.; Simonsen, A.; Hummer, G.; Đikić, I.: TBK1-mediated phosphorylation of LC3C and GABARAP-L2 controls autophagosome shedding by ATG4 protease. EMBO Reports 21 (1), e48317 (2019)

Siggel, M.; Bhaskara, R. M.; Hummer, G.: Phospholipid Scramblases Remodel the Shape of Asymmetric Membranes. The Journal of Physical Chemistry Letters 10 (20), pp. 6351 - 6354 (2019)

Covino, R.; Woodside, M. T.; Hummer, G.; Szabo, A.; Cossio, P.: Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors. The Journal of Chemical Physics 151 (15), 154115 (2019)

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)

Nishimura, T.; Gecht, M.; Covino, R.; Hummer, G.; Surma, M. A.; Klose, C.; Arai, H.; Kono, N.; Stefan, C. J.: Osh Proteins Control Nanoscale Lipid Organization Necessary for PI(4,5)P₂ Synthesis. Molecular Cell 75 (5), pp. 1043 - 1057 (2019)

Ochoa, R.; Laio, A.; Cossio, P.: Predicting the Affinity of Peptides to Major Histocompatibility Complex Class II by Scoring Molecular Dynamics Simulations. Journal of Chemical Information and Modeling 59 (8), pp. 3464 - 3473 (2019)

Bahrami, A.; Bahrami, A. H.: Vesicle constriction by rings of Janus nanoparticles and aggregates of curved proteins. Nanotechnology 30 (34), 345101 (2019)

Hofmann, S.; Januliene, D.; Mehdipour, A. R.; Thomas, C.; Stefan, E.; Brüchert, S.; Kuhn, B. T.; Geertsma, E. R.; Hummer, G.; Tampé, R. et al.; Möller, A.: Conformation space of a heterodimeric ABC exporter under turnover conditions. Nature 571 (7766), pp. 580 - 583 (2019)

Vögele, M.; Bhaskara, R.; Mulvihill, E.; van Pee, K.; Yildiz, Ö.; Kühlbrandt, W.; Müller, D. J.; Hummer, G.: Membrane perforation by the pore-forming toxin pneumolysin. Proceedings of the National Academy of Sciences of the United States of America 116 (27), pp. 13352 - 13357 (2019)

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)

Zakrzewska, S.; Mehdipour, A. R.; Malviya, V. N.; Nonaka, T.; Koepke, J.; Muenke, C.; Hausner, W.; Hummer, G.; Safarian, S.; Michel, H.: Inward-facing conformation of a multidrug resistance MATE family transporter. Proceedings of the National Academy of Sciences of the United States of America 116 (25), pp. 12275 - 12284 (2019)

Bhaskara, R.; Grumati, P.; Garcia-Pardo, J.; Kalayil, S.; Covarrubias-Pinto, A.; Chen, W.; Kudryashev, M.; Đikić, I.; Hummer, G.: Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy. Nature Communications 10, 2370 (2019)

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)

von Bülow, S.; Siggel, M.; Linke, M.; Hummer, G.: Dynamic cluster formation determines viscosity and diffusion in dense protein solutions. Proceedings of the National Academy of Sciences of the United States of America 116 (20), pp. 9843 - 9852 (2019)

Chang, Y.-N.; Jaumann, E. A.; Reichel, K.; Hartmann, J.; Oliver, D.; Hummer, G.: Structural basis for functional interactions in dimers of SLC26 transporters. Nature Communications 10, 2032 (2019)

van Lin, S. R.; Grotz, K. K.; Siretanu, I.; Schwierz, N.; Mugele, F.: Ion-Specific and pH-Dependent Hydration of Mica-Electrolyte Interfaces. Langmuir 35 (17), pp. 5737 - 5745 (2019)

Okazaki, K.-i.; Wöhlert, D.; Warnau, J.; Jung, H.; Yildiz, Ö.; Kühlbrandt, W.; Hummer, G.: Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting. Nature Communications 10, 1742 (2019)

Perez, C.; Mehdipour, A. R.; Hummer, G.; Locher, K. P.: Structure of Outward-Facing PglK and Molecular Dynamics of Lipid-Linked Oligosaccharide Recognition and Translocation. Structure 27 (4), pp. 669 - 678.e5 (2019)

Palacio-Rodríguez, K.; Lans, I.; Cavasotto, C. N.; Cossio, P.: Exponential consensus ranking improves the outcome in docking and receptor ensemble docking. Scientific Reports 9, 5142, pp. 1 - 14 (2019)

von Domaros, M.; Bratko, D.; Kirchner, B.; Hummer, G.; Luzar, A.: Multifaceted Water Dynamics in Spherical Nanocages. The Journal of Physical Chemistry C 123 (10), pp. 5989 - 5998 (2019)

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)

Chang, C.; Young, L. N.; Morris, K. L.; Bülow, S. v.; Schöneberg, J.; Yamamoto-Imoto, H.; Oe, Y.; Yamamoto, K.; Nakamura, S.; Stjepanovic, G. et al.; Hummer, G.; Yoshimori, T.; Hurley, J. H.: Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics. Molecular Cell 73 (2), pp. 339 - 353 (2019)

Böger, C.; Baldering, T. N.; Krüger, C. L.; Harwardt, M.-L. I. E.; Mertinkus, K. R.; Schröder, M. S.; Karathanasis, C.; Deußner-Helfmann, N. S.; Barth, H.-D.; Malkusch, S. et al.; Dietz, M. S.; Hummer, G.; Wohland, T.; Heilemann, M.: Quantification of membrane receptor complexes with single-molecule localization microscopy. Proceedings of SPIE 10884, 108840T (2019)

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)

Warnau, J.: Computational Studies of Membrane-bound Proteins Na⁺/H⁺-Antiporter and Respiratory Complex I. Dissertation, 97 pp., Fakultät für Chemie, Technische Universität München, Garching bei München (2019)

Vögele, M.: Theory and Simulation of Diffusion and Self-Assembly in Lipid Membranes. Dissertation, 242 pp., Fachbereich 13 (Physik), Goethe-Universität Frankfurt, Frankfurt am Main (2019)

Gemeinhardt, T. M.: Transport mechanism of the SLC23 transporter family. Master, 114 pp., Fachbereich 14 (Biochemie, Chemie, Pharmazie), Goethe-Universität Frankfurt, Frankfurt am Main (2019)

Jung, H.: Automatically discovering molecular reaction mechanisms. Master, 96 pp., Fachbereich Physik, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main (2019)