Max Planck Institute of Biophysics

Gerhard Hummer: Theoretical Biophysics – Department Publications

Journal Article (213)

2023

Journal Article

Flores-Solis, D.; Lushpinskaia, I. P.; Polyansky, A. A.; Changiarath, A.; Boehning, M.; Mirkovic, M.; Walshe, J.; Pietrek, L. M.; Cramer, P.; Stelzl, L. S. et al.; Zagrovic, B.; Zweckstetter, M.: Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II. Nature Communications 14, 5979 (2023)

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Journal Article

Oosterheert, W.; Blanc, F. E. C.; Roy, A.; Belyy, A.; Sanders, M. B.; Hofnagel, O.; Hummer, G.; Bieling, P.; Raunser, S.: Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments. Nature Structural & Molecular Biology (2023)

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Journal Article

Nguyen, H.; Nguyen, H. L.; Lan, P. D.; Thai, N. Q.; Sikora, M.; Li, M. S.: Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chemical Society Reviews (2023)

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Journal Article

Hanson, S. M.; Scholüke, J.; Liewald, J.; Sharma, R.; Ruse, C.; Engel, M.; Schüler, C.; Klaus, A.; Arghittu, S.; Baumbach, F. et al.; Seidenthal, M.; Dill, H.; Hummer, G.; Gottschalk, A.: Structure-function analysis suggests that the photoreceptor LITE-1 is a light-activated ion channel. Current biology: CB (2023)

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Journal Article

Goretzki, B.; Wiedemann, C.; McCray, B. A.; Schäfer, S. L.; Jansen, J.; Tebbe, F.; Mitrovic, S.-A.; Nöth, J.; Cabezudo, A. C.; Donohue, J. K. et al.; Jeffries, C. M.; Steinchen, W.; Stengel, F.; Sumner, C. J.; Hummer, G.; Hellmich, U. A.: Crosstalk between regulatory elements in disordered TRPV4 N-terminus modulates lipid-dependent channel activity. Nature Communications 14, 4165 (2023)

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Journal Article

Ibrahim, M.; Gilbert, J.; Heinz, M.; Nylander, T.; Schwierz, N.: Structural insights on ionizable Dlin-MC3-DMA lipids in DOPC layers by combining accurate atomistic force fields, molecular dynamics simulations and neutron reflectivity. Nanoscale 15 (2023)

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Journal Article

Bullerjahn, J. T.; von Bülow, S.; Heidari, M.; Hénin, J.; Hummer, G.: Unwrapping NPT Simulations to Calculate Diffusion Coefficients. Journal of Chemical Theory and Computation (2023)

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Journal Article

Valko, A.; Fracchiolla, D.: “Autophagic landscapes: on the paradox of survival through self-degradation” – A science-inspired exhibition. Autophagy 19 (9), pp. 2601 - 2606 (2023)

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Journal Article

Cai, W.; Jäger, M.; Bullerjahn, J. T.; Hugel, T.; Wolf, S.; Balzer, B. N.: Anisotropic Friction in a Ligand-Protein Complex. Nano Letters 23 (10), pp. 4111 - 4119 (2023)

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Foronda, H.; Fu, Y.; Covarrubias-Pinto, A.; Bocker, H. T.; González, A.; Seemann, E.; Franzka, P.; Bock, A.; Bhaskara, R. M.; Liebmann, L. et al.; Hoffmann, M. E.; Katona, I.; Koch, N.; Weis, J.; Kurth, I.; Gleeson, J. G.; Reggiori, F.; Hummer, G.; Kessels, M. M.; Qualmann, B.; Mari, M.; Dikić, I.; Hübner, C. A.: Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy. Nature (2023)

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González, A.; Covarrubias-Pinto, A.; Bhaskara, R. M.; Glogger, M.; Kuncha, S. K.; Xavier, A.; Seemann, E.; Misra, M.; Hoffmann, M. E.; Bräuning, B. et al.; Balakrishnan, A.; Qualmann, B.; Dötsch, V.; Schulman, B. A.; Kessels, M. M.; Hübner, C. A.; Heilemann, M.; Hummer, G.; Dikić, I.: Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum. Nature, pp. 1 - 8 (2023)

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Journal Article

Lettl, C.; Schindele, F.; Mehdipour, A. R.; Steiner, T.; Ring, D.; Brack-Werner, R.; Stecher, B.; Eisenreich, W.; Bilitewski, U.; Hummer, G. et al.; Witschel, M.; Fischer, W.; Haas, R.: Selective killing of the human gastric pathogen Helicobacter pylori by mitochondrial respiratory complex I inhibitors. Cell Chemical Biology 30 (5), pp. 499 - 512 (2023)

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Journal Article

Yu, M.; Heidari, M.; Mikhaleva, S.; Tan, P. S.; Mingu, S.; Ruan, H.; Reinkemeier, C. D.; Obarska-Kosinska, A.; Siggel, M.; Beck, M. et al.; Hummer, G.; Lemke, E. A.: Visualizing the disordered nuclear transport machinery in situ. Nature (2023)

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Journal Article

Jung, H.; Covino, R.; Arjun, A.; Leitold, C.; Dellago, C.; Bolhuis, P. G.; Hummer, G.: Machine-guided path sampling to discover mechanisms of molecular self-organization. Nature Computational Science 3 (4), pp. 334 - 345 (2023)

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Journal Article

Wu, D.; Mehdipour, A. R.; Finke, F.; Goojani, H. G.; Groh, R. R.; Grund, T. N.; Reichhart, T. M. B.; Zimmermann, R.; Welsch, S.; Bald, D. et al.; Shepherd, M.; Hummer, G.; Safarian, S.: Dissecting the conformational complexity and mechanism of a bacterial heme transporter. Nature Chemical Biology 10, pp. 1 - 12 (2023)

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Journal Article

Fábián, B.; Thallmair, S.; Hummer, G.: Optimal Bond Constraint Topology for Molecular Dynamics Simulations of Cholesterol. Journal of Chemical Theory and Computation 19 (5), pp. 1592 - 1601 (2023)

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Journal Article

Pietrek, L. M.; Stelzl, L. S.; Hummer, G.: Structural ensembles of disordered proteins from hierarchical chain growth and simulation. Current Opinion in Structural Biology 78, 102501 (2023)

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Journal Article

von Bülow, S.; Sikora, M.; Blanc, F. E. C.; Covino, R.; Hummer, G.: Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants. PLoS Computational Biology 19 (1), e1010822 (2023)

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Journal Article

Honti, B.; Fábián, B.; Idrissi, A.; Jedlovszky, P.: Surface Properties of N,N-Dimethylformamide-Water Mixtures, As Seen from Computer Simulations. The Journal of Physical Chemistry B 127 (4), pp. 1050 - 1062 (2023)

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2022

Journal Article

Zhu, R.; Canena, D.; Sikora, M.; Klausberger, M.; Seferovic, H.; Mehdipour, A. R.; Hain, L.; Laurent, E.; Monteil, V.; Wirnsberger, G. et al.; Wieneke, R.; Tampé, R.; Kienzl, N. F.; Mach, L.; Mirazimi, A.; Oh, Y. J.; Penninger, J. M.; Hummer, G.; Hinterdorfer, P.: Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level. Nature Communications 13 (1), 7926 (2022)

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Journal Article

Jensen, L. E.; Rao, S.; Schuschnig, M.; Cada, A. K.; Martens, S.; Hummer, G.; Hurley, J. H.: Membrane curvature sensing and stabilization by the autophagic LC3 lipidation machinery. Science Advances 8 (50), eadd1436 (2022)

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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)

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Journal Article

Schaefer, S. L.; Hummer, G.: Sublytic gasdermin-D pores captured in atomistic molecular simulations. eLife 11, e81432 (2022)

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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)

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Journal Article

Cruz-León, S.; Schwierz, N.: RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations. The Journal of Physical Chemistry B (2022)

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Journal Article

Bieber, A.; Capitanio, C.; Erdmann, P. S.; Fiedler, F.; Beck, F.; Lee, C.-W.; Li, D.; Hummer, G.; Schulman, B. A.; Baumeister, W. et al.; Wilfling, F.: In situ structural analysis reveals membrane shape transitions during autophagosome formation. Proceedings of the National Academy of Sciences of the United States of America 119 (39), e2209823119 (2022)

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Journal Article

Khera, R.; Mehdipour, A. R.; Bolla, J. R.; Kahnt, J.; Welsch, S.; Ermler, U.; Münke, C.; Robinson, C. V.; Hummer, G.; Xie, H. et al.; Michel, H.: Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism. The EMBO Journal 41 (18), e109990 (2022)

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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 (2022)

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Journal Article

Mikolajczyk, K.; Sikora, M.; Hanus, C.; Kaczmarek, R.; Czerwinski, M.: One of the two N-glycans on the human Gb3/CD77 synthase is essential for its activity and allosterically regulates its function. Biochemical and Biophysical Research Communications (Orlando, FL) 617, pp. 36 - 41 (2022)

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Journal Article

Palacio-Rodriguez, K.; Vroylandt, H.; Stelzl, L. S.; Pietrucci, F.; Hummer, G.; Cossio, P.: Transition Rates and Efficiency of Collective Variables from Time-Dependent Biased Simulations. The Journal of Physical Chemistry Letters 13 (32), pp. 7490 - 7496 (2022)

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Journal Article

Sušac, L.; Vuong, M. T.; Thomas, C.; von Bülow, S.; O'Brien-Ball, C.; Santos, A. M.; Fernandes, R. A.; Hummer, G.; Tampé, R.; Davis, S. J.: Structure of a fully assembled tumor-specific T cell receptor ligated by pMHC. Cell 185 (17), pp. 3201 - 3213 (2022)

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publisher-version

Journal Article

Bullerjahn, J. T.; Hummer, G.: Reversible bond kinetics from single-molecule force spectroscopy experiments close to equilibrium. Physical Review Research 4 (3), 033097 (2022)

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Journal Article

Fábián, B.; Thallmair, S.; Hummer, G.: Small ionic radii limit time step in Martini 3 molecular dynamics simulations. The Journal of Chemical Physics 157 (3), 034101 (2022)

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Journal Article

Cruz-León, S.; Vanderlinden, W.; Müller, P.; Forster, T.; Staudt, G.; Lin, Y.-Y.; Lipfert, J.; Schwierz, N.: Twisting DNA by salt. Nucleic Acids Research (London) 50 (10), pp. 5726 - 5739 (2022)

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Journal Article

Mosalaganti, S.; Obarska-Kosinska, A.; Siggel, M.; Taniguchi, R.; Turoňová, B.; Zimmerli, C. E.; Buczak, K.; Schmidt, F. H.; Margiotta, E.; Mackmull, M.-T. et al.; Hagen, W. J. H.; Hummer, G.; Kosinski, J.; Beck, M.: AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science 376 (6598), eabm9506 (2022)

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Journal Article

Cullati, S. N.; Chaikuad, A.; Chen, J.-S.; Gebel, J.; Tesmer, L.; Zhubi, R.; Navarrete-Perea, J.; Guillen, R. X.; Gygi, S. P.; Hummer, G. et al.; Dötsch, V.; Knapp, S.; Gould, K. L.: Kinase domain autophosphorylation rewires the activity and substrate specificity of CK1 enzymes. Molecular Cell 82 (11), pp. 2006 - 2020.e8 (2022)

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Journal Article

Ochoa, R.; Lunardelli, V. A. S.; Rosa, D. S.; Laio, A.; Cossio, P.: Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol. Frontiers in immunology 13, 862851 (2022)

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Journal Article

Cai, W.; Bullerjahn, J. T.; Lallemang, M.; Kroy, K.; Balzer, B. N.; Hugel, T.: Angle-dependent strength of a single chemical bond by stereographic force spectroscopy. Chemical Science 13 (19), pp. 5734 - 5740 (2022)

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Journal Article

Fuks, C.; Falkner, S.; Schwierz, N.; Hengesbach, M.: Combining Coarse-Grained Simulations and Single Molecule Analysis Reveals a Three-State Folding Model of the Guanidine-II Riboswitch. Frontiers in Molecular Biosciences 9, 826505 (2022)

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Journal Article

Grotz, K. K.; Schwierz, N.: Magnesium force fields for OPC water with accurate solvation, ion-binding, and water-exchange properties: Successful transfer from SPC/E. The Journal of Chemical Physics 156 (11), 114501 (2022)

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Journal Article

Seidel, M.; Becker, A.; Pereira, F.; Landry, J. J. M.; de Azevedo, N. T. D.; Fusco, C. M.; Kaindl, E.; Romanov, N.; Baumbach, J.; Langer, J. D. et al.; Schuman, E. M.; Patil, K. R.; Hummer, G.; Benes, V.; Beck, M.: Co-translational assembly orchestrates competing biogenesis pathways. Nature Communications 13, 1224 (2022)

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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)

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Journal Article

Lambert, E.; Mehdipour, A. R.; Schmidt, A.; Hummer, G.; Perez, C.: Evidence for a trap-and-flip mechanism in a proton-dependent lipid transporter. Nature Communications 13 (1), 1022 (2022)

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Journal Article

Slováková, J.; Sikora, M.; Arslan, F. N.; Caballero-Mancebo, S.; Krens, S. F. G.; Kaufmann, W. A.; Merrin, J.; Heisenberg, C.-P.: Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America 119 (8), e2122030119 (2022)

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Journal Article

Neumann, J.; Schwierz, N.: Artificial Intelligence Resolves Kinetic Pathways of Magnesium Binding to RNA. Journal of Chemical Theory and Computation 18 (2), pp. 1202 - 1212 (2022)

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Journal Article

Gruijs da Silva, L. A.; Simonetti, F.; Hutten, S.; Riemenschneider, H.; Sternburg, E. L.; Pietrek, L. M.; Gebel, J.; Dötsch, V.; Edbauer, D.; Hummer, G. et al.; Stelzl, L. S.; Dormann, D.: Disease-linked TDP-43 hyperphosphorylation suppresses TDP-43 condensation and aggregation. EMBO Journal 41 (3), e108443 (2022)

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Journal Article

Grotz, K. K.; Schwierz, N.: Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D. Journal of Chemical Theory and Computation 18 (1), pp. 526 - 537 (2022)

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Journal Article

Heerde, T.; Rennegarbe, M.; Biedermann, A.; Savran, D.; Pfeiffer, P. B.; Hitzenberger, M.; Baur, J.; Puscalau-Girtu, I.; Zacharias, M.; Schwierz, N. et al.; Haupt, C.; Schmidt, M.; Fändrich, M.: Cryo-EM demonstrates the in vitro proliferation of an ex vivo amyloid fibril morphology by seeding. Nature Communications 13 (1), 85 (2022)

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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)

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Journal Article

Zimmerli, C. E.; Allegretti, M.; Rantos, V.; Goetz, S. K.; Obarska-Kosinska, A.; Zagoriy, I.; Halavatyi, A.; Hummer, G.; Mahamid, J.; Kosinski, J. et al.; Beck, M.: Nuclear pores dilate and constrict in cellulo. Science 374 (6573), eabd9776 (2021)

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Journal Article

Sim, S. I.; von Bülow, S.; Hummer, G.; Park, E.: Structural basis of polyamine transport by human ATP13A2 (PARK9). Molecular Cell 81, pp. 4635 - 4649 (2021)

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Journal Article

Zhao, J.; Xie, H.; Mehdipour, A. R.; Safarian, S.; Ermler, U.; Münke, C.; Thielmann, Y.; Hummer, G.; Ebersberger, I.; Wang, J. et al.; Michel, H.: The structure of the Aquifex aeolicus MATE family multidrug resistance transporter and sequence comparisons suggest the existence of a new subfamily. Proceedings of the National Academy of Sciences of the United States of America 118 (46), e2107335118 (2021)

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Journal Article

Rocha-Roa, C.; Orjuela, J. D.; Leidy, C.; Cossio, P.; Aponte-Santamaría, C.: Cardiolipin prevents pore formation in phosphatidylglycerol bacterial membrane models. FEBS Letters 595 (21), pp. 2701 - 2714 (2021)

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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)

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Journal Article

Müller, D. J.; Dumitru, A. C.; Lo Giudice, C.; Gaub, H. E.; Hinterdorfer, P.; Hummer, G.; De Yoreo, J. J.; Dufrêne, Y. F.; Alsteens, D.: Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems. Chemical Reviews 121 (19), pp. 11701 - 11725 (2021)

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Journal Article

Reggio, A.; Buonomo, V.; Berkane, R.; Bhaskara, R.; Tellechea, M.; Peluso, I.; Polishchuk, E.; Di Lorenzo, G.; Cirillov, C.; Esposito, M. et al.; Hussain, A.; Huebner, A. K.; Hübner, C. A.; Settembre, C.; Hummer, G.; Grumati, P.; Stolz, A.: Role of FAM134 paralogues in endoplasmic reticulum remodeling, ER-phagy, and Collagen quality control. EMBO Reports 22 (9), e52289 (2021)

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Journal Article

Safarian, S.; Opel-Reading, H. K.; Wu, D.; Mehdipour, A. R.; Hards, K.; Harold, L. H.; Radloff, M.; Stewart, I.; Welsch, S.; Hummer, G. et al.; Cook, G. M.; Krause, K. L.; Michel, H.: The cryo-EM structure of the bd oxidase from M. tuberculosis reveals a unique structural framework and enables rational drug design to combat TB. Nature Communications 12 (1), 5236 (2021)

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Journal Article

Falkner, S.; Schwierz, N.: Kinetic pathways of water exchange in the first hydration shell of magnesium: Influence of water model and ionic force field. The Journal of Chemical Physics 155 (8), 084503 (2021)

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Journal Article

Väth, K.; Mattes, C.; Reinhard, J.; Covino, R.; Stumpf, H.; Hummer, G.; Ernst, R.: Cysteine cross-linking in native membranes establishes the transmembrane architecture of Ire1. The Journal of Cell Biology 220 (8), e202011078 (2021)

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Journal Article

Mukherjee, R.; Bhattacharya, A.; Bojkova, D.; Mehdipour, A. R.; Shin, D.; Khan, K. S.; Hei-Yin Cheung, H.; Wong, K.-B.; Ng, W.; Cinatl, J. et al.; Geurink, P. P.; van der Heden van Noort, G. J.; Rajalingam, K.; Ciesek, S.; Hummer, G.; Dikic, I.: Famotidine inhibits Toll-like receptor 3-mediated inflammatory signaling in SARS-CoV2 infection. The Journal of Biological Chemistry 297 (2), 100925 (2021)

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Journal Article

Schaefer, S. L.; Jung, H.; Hummer, G.: Binding of SARS-CoV-2 Fusion Peptide to Host Endosome and Plasma Membrane. The Journal of Physical Chemistry B 125 (28), pp. 7732 - 7741 (2021)

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Journal Article

Giraldo-Barreto, J.; Ortiz, S.; Thiede, E. H.; Palacio-Rodriguez, K.; Carpenter, B.; Barnett, A. H.; Cossio, P.: A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments. Scientific Reports 11 (1), 13657 (2021)

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Journal Article

Bullerjahn, J. T.; Hummer, G.: Maximum likelihood estimates of diffusion coefficients from single-particle tracking experiments. The Journal of Chemical Physics 154 (23), 234105 (2021)

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Journal Article

Mehdipour, A. R.; Hummer, G.: Dual nature of human ACE2 glycosylation in binding to SARS-CoV-2 spike. Proceedings of the National Academy of Sciences of the United States of America 118 (19), e2100425118 (2021)

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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)

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Journal Article

Cruz-León, S.; Grotz, K. K.; Schwierz, N.: Extended magnesium and calcium force field parameters for accurate ion–nucleic acid interactions in biomolecular simulations. The Journal of Chemical Physics 154 (17), 171102 (2021)

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Journal Article

Grotz, K. K.; Cruz-León, S.; Schwierz, N.: Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties. Journal of Chemical Theory and Computation 17 (4), pp. 2530 - 2540 (2021)

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Journal Article

Nome, R. A.; Cossio, P.; Z, Y.: Editorial: Integrating Timescales From Molecules Up. Frontiers in Chemistry 9, 680533 (2021)

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Journal Article

Sikora, M.; von Bülow, S.; Blanc, F. E. C.; Gecht, M.; Covino, R.; Hummer, G.: Computational epitope map of SARS-CoV-2 spike protein. PLoS Computational Biology 17 (4), e1008790 (2021)

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Journal Article

Ochoa, R.; Laskowski, R. A.; Thornton, J. M.; Cossio, P.: Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide Binders. Frontiers in Molecular Biosciences 8, 636562 (2021)

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Journal Article

Ochoa, R.; Cossio, P.: PepFun: Open Source Protocols for Peptide-Related Computational Analysis. Molecules 26 (6), 1664 (2021)

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Journal Article

Siggel, M.; Bhaskara, R.; Moesser, M. K.; Đikić, I.; Hummer, G.: FAM134B-RHD Protein Clustering Drives Spontaneous Budding of Asymmetric Membranes. The Journal of Physical Chemistry Letters 12 (7), pp. 1926 - 1931 (2021)

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Journal Article

Benayad, Z.; von Bülow, S.; Stelzl, L. S.; Hummer, G.: Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model. Journal of Chemical Theory and Computation 17 (1), pp. 525 - 537 (2021)

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Journal Article

Bárcena, M.; Barnes, C. O.; Beck, M.; Bjorkman, P. J.; Canard, B.; Gao, G. F.; Gao, Y.; Hilgenfeld, R.; Hummer, G.; Patwardhan, A. et al.; Santoni, G.; Saphire, E. O.; Schaffitzel, C.; Schendel, S. L.; Smith, J. L.; Thorn, A.; Veesler, D.; Zhang, P.; Zhou, Q.: Structural biology in the fight against COVID-19. Nature Structural and Molecular Biology 28 (1), pp. 2 - 7 (2021)

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Journal Article

Klionsky, D. J.; Abdel-Aziz, A. K.; Abdelfatah, S.; Hummer, G.; 2295 other, A.: Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy 17 (1), pp. 1 - 382 (2021)

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2020

Journal Article

Ochoa, R.; Magnitov, M.; Laskowski, R. A.; Cossio, P.; Thornton, J. M.: An automated protocol for modelling peptide substrates to proteases. BMC Bioinformatics 21 (1), 586 (2020)

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Journal Article

Collauto, A.; von Bülow, S.; Gophane, D.; Saha, S.; Stelzl, L. S.; Hummer, G.; Sigurdsson, S. T.; Prisner, T.: Compaction of RNA duplexes in the cell. Angewandte Chemie, International Edition in English 59, pp. 23025 - 23029 (2020)

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Journal Article

Shin, D.; Mukherjee, R.; Grewe, D.; Bojkova, D.; Baek, K.; Bhattacharya, A.; Schulz, L.; Widera, M.; Mehdipour, A. R.; Tascher, G. et al.; Geurink, P. P.; Wilhelm, A.; van der Heden van Noort, G. J.; Ovaa, H.; Müller, S.; Knobeloch, K.-P.; Rajalingam, K.; Schulman, B.; Cinatl, J.; Hummer, G.; Ciesek, S.; Đikić, I.: Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature 587 (7835), pp. 657 - 662 (2020)

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Journal Article

Shin, D.; Bhattacharya, A.; Cheng, Y.-L.; Alonso, M. C.; Mehdipour, A. R.; van der Heden van Noort, G. J.; Ovaa, H.; Hummer, G.; Dikic, I.: Bacterial OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection. eLife 9 (2020)

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Journal Article

Sikora, M.; Ermel, U. H.; Seybold, A.; Kunz, M.; Calloni, G.; Reitz, J.; Vabulas, R. M.; Hummer, G.; Frangakis, A. S.: Desmosome architecture derived from molecular dynamics simulations and cryo-electron tomography. Proceedings of the National Academy of Sciences of the United States of America 117 (44), pp. 27132 - 27140 (2020)

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Journal Article

Turoňová, B.; Sikora, M.; Schürmann, C.; Hagen, W. J. H.; Welsch, S.; Blanc, F. E. C.; von Bülow, S.; Gecht, M.; Bagola, K.; Hörner, C. et al.; van Zandbergen, G.; Landry, J.; de Azevedo, N. T. D.; Mosalaganti, S.; Schwarz, A.; Covino, R.; Mühlebach, M. D.; Hummer, G.; Krijnse Locker, J.; Beck, M.: In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. Science 370 (6513), pp. 203 - 208 (2020)

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Gebel, J.; Tuppi, M.; Chaikuad, A.; Hötte, K.; Schröder, M.; Schulz, L.; Löhr, F.; Gutfreund, N.; Finke, F.; Henrich, E. et al.; Mezhyrova, J.; Lehnert, R.; Pampaloni, F.; Hummer, G.; Stelzer, E. H.K.; Knapp, S.; Dötsch, V.: p63 uses a switch-like mechanism to set the threshold for induction of apoptosis. Nature Chemical Biology 16 (10), pp. 1078 - 1086 (2020)

MPG.PuRe

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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)

MPG.PuRe

Journal Article

Lans, I.; Palacio-Rodríguez, K.; Cavasotto, C. N.; Cossio, P.: Flexi-pharma: a molecule-ranking strategy for virtual screening using pharmacophores from ligand-free conformational ensembles. Journal of Computer-Aided Molecular Design 34 (10), pp. 1063 - 1077 (2020)

MPG.PuRe

Journal Article

Mykuliak, V. V.; Sikora, M.; Booth, J. J.; Cieplak, M.; Shalashilin, D. V.; Hytönen, V. P.: Mechanical Unfolding of Proteins - A Comparative Nonequilibrium Molecular Dynamics Study. Biophysical Journal 119, pp. 939 - 949 (2020)

MPG.PuRe

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Sawa-Makarska, J.; Baumann, V.; Coudevylle, N.; von Bülow, S.; Nogellova, V.; Abert, C.; Schuschnig, M.; Graef, M.; Hummer, G.; Martens, S.: Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation. Science 369 (6508), eaaz7714 (2020)

MPG.PuRe

Journal Article

Lans, I.; Anoz-Carbonell, E.; Palacio-Rodríguez, K.; Aínsa, J. A.; Medina, M.; Cossio, P.: In silico discovery and biological validation of ligands of FAD synthase, a promising new antimicrobial target. PLoS Computational Biology 16 (8), e1007898 (2020)

MPG.PuRe

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Ortiz , S.; Stanisic, L.; Rodriguez , B. A.; Rampp, M.; Hummer, G.; Cossio, P.: Validation tests for cryo-EM maps using an independent particle set. Journal of Structural Biology: X 4, 100032 (2020)

MPG.PuRe

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Bullerjahn, J. T.; von Bülow, S.; Hummer, G.: Optimal estimates of self-diffusion coefficients from molecular dynamics simulations. The Journal of Chemical Physics 153 (2), 024116 (2020)

MPG.PuRe

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von Bülow, S.; Bullerjahn, J. T.; Hummer, G.: Systematic errors in diffusion coefficients from long-time molecular dynamics simulations at constant pressure. The Journal of Chemical Physics 153 (2), 021101 (2020)

MPG.PuRe

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Schwierz, N.: Kinetic pathways of water exchange in the first hydration shell of magnesium. The Journal of Chemical Physics 152 (22), 224106 (2020)

MPG.PuRe

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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)

MPG.PuRe

Journal Article

Cruz-León, S.; Schwierz, N.: Hofmeister Series for Metal-Cation-RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics. Langmuir 36 (21), pp. 5979 - 5989 (2020)

MPG.PuRe

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Cossio, P.: Need for Cross-Validation of Single Particle Cryo-EM. Journal of Chemical Information and Modeling 60 (5), pp. 2413 - 2418 (2020)

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Wu, X.; Siggel, M.; Ovchinnikov, S.; Mi, W.; Svetlov, V.; Nudler, E.; Liao, M.; Hummer, G.; Rapoport, T. A.: Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. Science 368 (6489), eaaz2449, p. 385 (2020)

MPG.PuRe

Journal Article

Vögele, M.; Bhaskara, R.; Mulvihill, E.; van Pee, K.; Yildiz, Ö.; Kühlbrandt, W.; Müller, D. J.; Hummer, G.: Reply to Desikan et al.: Micelle formation among various mechanisms of toxin pore formation. Proceedings of the National Academy of Sciences of the United States of America 117 (10), pp. 5109 - 5110 (2020)

MPG.PuRe

Journal Article

Ballweg, S.; Sezgin, E.; Doktorova, M.; Covino, R.; Reinhard, J.; Wunnicke, D.; Hänelt, I.; Levental, I.; Hummer, G.; Ernst, R.: Regulation of lipid saturation without sensing membrane fluidity. Nature Communications 11, 756 (2020)

MPG.PuRe

Journal Article

Heinz, M.; Erlenbach, N.; Stelzl, L. S.; Thierolf, G.; Kamble, N. R.; Sigurdsson, S. T. H.; Prisner, T. F.; Hummer, G.: High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label. Nucleic Acids Research 48 (2), pp. 924 - 933 (2020)

MPG.PuRe

Journal Article

Warnau, J.; Wöhlert, D.; Okazaki, K.-I.; Yildiz, Ö.; Gamiz-Hernandez, A. P.; Kaila, V. R. I.; Kühlbrandt, W.; Hummer, G.: Ion Binding and Selectivity of the Na⁺/H⁺ Antiporter MjNhaP1 from Experiment and Simulation. The Journal of Physical Chemistry B 124 (2), pp. 336 - 344 (2020)

MPG.PuRe