Gerhard Hummer: Theoretical Biophysics – Department Publications | Max Planck Institute of Biophysics

Max Planck Institute of Biophysics

Journal Article (233)

2020

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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Journal Article

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)

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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)

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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)

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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)

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Journal Article

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)

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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)

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Journal Article

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)

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Journal Article

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)

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Journal Article

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)

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Journal Article

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

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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)

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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)

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Journal Article

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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Journal Article

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)

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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)

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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)

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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)

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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)

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Journal Article

Pietrek, L. M.; Stelzl, L. S.; Hummer, G.: Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 16 (1), pp. 725 - 737 (2020)

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Journal Article

Shin, D.; Mukherjee, R.; Liu, Y.; Gonzalez, A.; Bonn, F.; Liu, Y.; Rogov, V. V.; Heinz, M.; Stolz, A.; Hummer, G. et al.; Dötsch, V.; Luo, Z.-Q.; Bhogaraju, S.; Đikić, I.: Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB. Molecular Cell 77 (1), pp. 164 - 179 (2020)

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2019

Journal Article

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)

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Journal Article

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)

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Journal Article

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)

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Journal Article

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)

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Journal Article

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)

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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)

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Journal Article

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)

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Journal Article

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)

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Journal Article

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

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Journal Article

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)

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Journal Article

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)

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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)

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Journal Article

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)

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Journal Article

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)

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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)

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Journal Article

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)

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Journal Article

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)

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Journal Article

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)

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Journal Article

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)

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Journal Article

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)

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Journal Article

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)

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Journal Article

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)

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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)

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Journal Article

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)

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Journal Article

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)

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2018

Journal Article

Schöneberg, J.; Pavlin, M. R.; Yan, S.; Righini, M.; Lee, I.-H.; Carlson, L.-A.; Bahrami, A. H.; Goldman, D. H.; Ren, X.; Hummer, G. et al.; Bustamante, C.; Hurley, J. H.: ATP-dependent force generation and membrane scission by ESCRT-III and Vps4. Science 362 (6421), pp. 1423 - 1428 (2018)

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Journal Article

Grotz, K. K.; Nueesch, M. F.; Holmstrom, E. D.; Heinz, M.; Stelzl, L. S.; Schuler, B.; Hummer, G.: Dispersion Correction Alleviates Dye Stacking of Single-Stranded DNA and RNA in Simulations of Single-Molecule Fluorescence Experiments. The Journal of Physical Chemistry B 122 (49), pp. 11626 - 11639 (2018)

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Journal Article

Seyfried, P.; Heinz, M.; Pintér, G.; Klötzner, D.-P.; Becker, Y.; Bolte, M.; Jonker, H. R. A.; Stelzl, L. S.; Hummer, G.; Schwalbe, H. et al.; Heckel, A.: Optimal Destabilization of DNA Double Strands by Single-Nucleobase Caging. Chemistry – A European Journal 24 (66), pp. 17568 - 17576 (2018)

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Journal Article

Bock, C.; Löhr, F.; Tumulka, F.; Reichel, K.; Würz, J.; Hummer, G.; Schäfer, L.; Tampé, R.; Joseph, B.; Bernhard, F. et al.; Dötsch, V.; Abele, R.: Structural and functional insights into the interaction and targeting hub TMD0 of the polypeptide transporter TAPL. Scientific Reports 8, 15662 (2018)

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Journal Article

Rossini, E.; Gajewski, J.; Klaus, M.; Hummer, G.; Grininger, M.: Analysis and engineering of substrate shuttling by the acyl carrier protein (ACP) in fatty acid synthases (FASs). Chemical Communications 54 (82), pp. 11606 - 11609 (2018)

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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)

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Journal Article

Cossio, P.; Allegretti, M.; Mayer, F.; Müller, V.; Vonck, J.; Hummer, G.: Bayesian inference of rotor ring stoichiometry from electron microscopy images of archaeal ATP synthase. Microscopy 67 (5), pp. 266 - 273 (2018)

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Journal Article

Lans, I.; Seco, J.; Serrano, A.; Burbano, R.; Cossio, P.; Daza, M. C.; Medina, M.: The Dimer-of-Trimers Assembly Prevents Catalysis at the Transferase Site of Prokaryotic FAD Synthase. Biophysical Journal 115 (6), pp. 988 - 995 (2018)

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Journal Article

Warnau, J.; Sharma, V.; Gamiz-Hernandez, A. P.; Di Luca, A.; Haapanen, O.; Vattulainen, I.; Wilkström, M.; Hummer, G.; Kaila, V. R. I.: Redox-coupled quinone dynamics in the respiratory complex I. Proceedings of the National Academy of Sciences of the United States of America 115 (36), pp. E8413 - E8420 (2018)

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Journal Article

Hofbauer, H. F.; Gecht, M.; Fischer, S. C.; Seybert, A.; Frangakis, A. S.; Stelzer, E. H. K.; Covino, R.; Hummer, G.; Ernst, R.: The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1. The Journal of Cell Biology: JCB 217 (9), pp. 3109 - 3126 (2018)

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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)

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Journal Article

Cruz-León, S.; Vázquez-Mayagoitia, A.; Melchionna, S.; Schwierz, N.; Fyta, M.: Coarse-Grained Double-Stranded RNA Model from Quantum-Mechanical Calculations. The Journal of Physical Chemistry B 122 (32), pp. 7915 - 7928 (2018)

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Journal Article

Gränz, M.; Erlenbach, N.; Spindler, P.; Gophane, D. B.; Stelzl, L. S.; Sigurdsson, S. T.; Prisner, T. F.: Dynamics of Nucleic Acids at Room Temperature Revealed by Pulsed EPR Spectroscopy. Angewandte Chemie International Edition 57 (33), pp. 10540 - 10543 (2018)

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Journal Article

Covino, R.; Hummer, G.; Ernst, R.: Integrated Functions of Membrane Property Sensors and a Hidden Side of the Unfolded Protein Response. Molecular Cell 71 (3), pp. 458 - 467 (2018)

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Journal Article

Vögele, M.; Köfinger, J.; Hummer, G.: Hydrodynamics of Diffusion in Lipid Membrane Simulations. Physical Review Letters 120 (26), 268104 (2018)

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Journal Article

De Vos, O.; Venable, R. M.; Van Hecke, T.; Hummer, G.; Pastor, R. W.; Ghysels, A.: Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model. Journal of Chemical Theory and Computation 14 (7), pp. 3811 - 3824 (2018)

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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)

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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)

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Journal Article

Ardevol, A.; Hummer, G.: Retinal isomerization and water-pore formation in channelrhodopsin-2. Proceedings of the National Academy of Sciences of the United States of America 115 (14), pp. 3557 - 3562 (2018)

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Journal Article

Cossio, P.; Hummer, G.: Likelihood-based structural analysis of electron microscopy images. Current Opinion in Structural Biology 49, pp. 162 - 168 (2018)

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Journal Article

Cossio, P.; Hummer, G.; Szabo, A.: Transition paths in single-molecule force spectroscopy. The Journal of Chemical Physics 148 (12), 123309 (2018)

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Journal Article

Rossini, E.; Bochevarov, A. D.; Knapp, E. W.: Empirical Conversion of pK_a Values between Different Solvents and Interpretation of the Parameters: Application to Water, Acetonitrile, Dimethyl Sulfoxide, and Methanol. ACS Omega 3 (2), pp. 1653 - 1662 (2018)

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Journal Article

Mamatkulov, S.; Schwierz, N.: Force fields for monovalent and divalent metal cations in TIP3P water based on thermodynamic and kinetic properties. The Journal of Chemical Physics 148 (7), 074504 (2018)

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Journal Article

Bahrami, A. H.; Weikl, T. R.: Curvature-Mediated Assembly of Janus Nanoparticles on Membrane Vesicles. Nano Letters 18 (2), pp. 1259 - 1263 (2018)

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Journal Article

Ramírez, A. S.; Boilevin, J.; Mehdipour, A. R.; Hummer, G.; Darbre, T.; Reymond, J.-L.; Locher, K. P.: Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase. Nature Communications 9, 445 (2018)

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Journal Article

Sebastián, M.; Anoz-Carbonell, E.; Gracia, B.; Cossio, P.; Aínsa, J. A.; Lans, I.; Medina, M.: Discovery of antimicrobial compounds targeting bacterial type FAD synthetases. Journal of Enzyme Inhibition and Medicinal Chemistry 33 (1), pp. 241 - 254 (2018)

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2017

Journal Article

D'Imprima, E.; Salzer, R.; Bhaskara, R. M.; Sánchez, R.; Rose, I.; Kirchner, L.; Hummer, G.; Kühlbrandt, W.; Vonck, J.; Averhoff, B.: Cryo-EM structure of the bifunctional secretin complex of Thermus thermophilus. eLife 6, 10.7554/eLife.30483 (2017)

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Journal Article

Stelzl, L. S.; Kells, A.; Rosta, E.; Hummer, G.: Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations. Journal of Chemical Theory and Computation 13 (12), pp. 6328 - 6342 (2017)

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Journal Article

Lazaridis, T.; Hummer, G.: Classical Molecular Dynamics with Mobile Protons. Journal of Chemical Information and Modeling 57 (11), pp. 2833 - 2845 (2017)

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Journal Article

Bahrami, A. H.; Lin, M. G.; Ren, X.; Hurley, J. H.; Hummer, G.: Scaffolding the cup-shaped double membrane in autophagy. PLoS Computational Biology 13 (10), e1005817 (2017)

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Journal Article

Jung, H.; Okazaki, K.-i.; Hummer, G.: Transition path sampling of rare events by shooting from the top. The Journal of Chemical Physics 147 (15), 152716 (2017)

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Journal Article

Leahy, C. T.; Kells, A.; Hummer, G.; Buchete, N.-V.; Rosta, E.: Peptide dimerization-dissociation rates from replica exchange molecular dynamics. The Journal of Chemical Physics 147 (15), 152725 (2017)

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Journal Article

Martini, L.; Covino, R.; Hummer, G.; Buchete, N.-V.; Rosta, E.: Variational Identification of Markovian Transition States. Physical Review X 7 (3), 031060 (2017)

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Journal Article

Bahrami, A. H.; Hummer, G.: Formation and Stability of Lipid Membrane Nanotubes. ACS Nano 11 (9), pp. 9558 - 9565 (2017)

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Journal Article

Sharma, V.; Belevich, G.; Gamiz-Hernandez, A. P.; Róg, T.; Vattulainen, I.; Verkhovskaya, M. L.; Wikström, M.; Hummer, G.; Kaila, V. R.I.: Redox-induced activation of the proton pump in the respiratory complex I. Proceedings of the National Academy of Sciences of the United States of America 112 (37), pp. 11571 - 11576 (2017)

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Journal Article

Stelzl, L. S.; Erlenbach, N.; Heinz, M.; Prisner, T. F.; Hummer, G.: Resolving the Conformational Dynamics of DNA with Ångstrom Resolution by Pulsed Electron–Electron Double Resonance and Molecular Dynamics. Journal of the American Chemical Society 139 (34), pp. 11674 - 11677 (2017)

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Journal Article

Halbleib, K.; Pesek, K.; Covino, R.; Hofbauer, H. F.; Wunnicke, D.; Hänelt, I.; Hummer, G.; Ernst, R.: Activation of the Unfolded Protein Response by Lipid Bilayer Stress. Molecular Cell 67 (4), pp. 673 - 684 (2017)

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Journal Article

Stelzl, L. S.; Hummer, G.: Kinetics from Replica Exchange Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 13 (8), pp. 3927 - 3935 (2017)

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Journal Article

Chiavazzo, E.; Covino, R.; Coifman, R. R.; Gear, C. W.; Georgiou, A. S.; Hummer, G.; Kevrekidis, I. G.: Intrinsic map dynamics exploration for uncharted effective free-energy landscapes. Proceedings of the National Academy of Sciences of the United States of America 114 (28), pp. E5494 - E5503 (2017)

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Journal Article

Malinverni, D.; Jost-Lopez, A.; De Los Rios, P.; Hummer, G.; Barducci, A.: Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and coevolutionary sequence analysis. eLife 6, e23471 (2017)

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Journal Article

Ghysels, A.; Venables, R. M.; Pastor, R. W.; Hummer, G.: Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes. Journal of Chemical Theory and Computation 13 (6), pp. 2962 - 2976 (2017)

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Journal Article

Reichel, K.; Fisette, O.; Braun, T.; Lange, O.; Hummer, G.; Schäfer, L. V.: Systematic evaluation of CS‐Rosetta for membrane protein structure prediction with sparse NOE restraints. Proteins: Structure, Function, and Bioinformatics 85 (5), pp. 812 - 826 (2017)

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Journal Article

Hummer, G.; Szabo, A.: Dynamics of the Orientational Factor in Fluorescence Resonance Energy Transfer. The Journal of Physical Chemistry B 121 (15), pp. 3331 - 3339 (2017)

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Journal Article

Karathanasis, C.; Frick, F.; Hummer, G.; Heilemann, M.: Molecule Counts in Localization Microscopy with Organic Fluorophores. ChemPhysChem 18 (8), pp. 942 - 948 (2017)

MPG.PuRe

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)

MPG.PuRe

Journal Article

Simonson, T.; Hummer, G.; Roux, B.: Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies. The Journal of Physical Chemistry A 121 (7), pp. 1525 - 1530 (2017)

MPG.PuRe

Journal Article

Schwierz, N.; Frost, C. V.; Geissler, P. L.; Zacharias, M.: From Aβ Filament to Fibril: Molecular Mechanism of Surface-Activated Secondary Nucleation from All-Atom MD Simulations. The Journal of Physical Chemistry B 121 (4), pp. 671 - 682 (2017)

MPG.PuRe

Journal Article

Nöll, A.; Christoph, T.; Herbring, V.; Zollmann, T.; Barth, K.; Mehdipour, A. R.; Tomasiak, T. M.; Brüchert, S.; Joseph, B.; Abele, R. et al.; Oliéric, V.; Wang, M.; Diederichs, K.; Hummer, G.; Stroud, R. M.; Pos, K. M.; Tampé, R.: Crystal structure and mechanistic basis of a functional homolog of the antigen transporter TAP. Proceedings of the National Academy of Sciences of the United States of America 114 (4), pp. E438 - E447 (2017)

MPG.PuRe

Journal Article

Cossio, P.; Rohr, D.; Baruffa, F.; Rampp, M.; Lindenstruth, V.; Hummer, G.: BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images. Computer Physics Communications 210 (01), pp. 163 - 171 (2017)

MPG.PuRe

Journal Article

Diskowski, M.; Mehdipour, A. R.; Wunnicke, D.; Mills, D. J.; Mikusevic, V.; Bärland, N.; Hoffmann, J.; Morgner, N.; Steinhoff, H.-J.; Hummer, G.: Helical jackknives control the gates of the double-pore K⁺ uptake system KtrABs. eLife, pp. 1 - 21 (2017)

MPG.PuRe

2016

Journal Article

Hummer, G.; Fricke, F.; Heilemann, M.: Model-independent counting of molecules in single-molecule localization microscopy. Molecular Biology of the Cell 27 (22), pp. 3637 - 3644 (2016)

MPG.PuRe

Journal Article

Lehnert, E.; Mao, J.; Mehdipour, A. R.; Hummer, G.; Abele, R.; Glaubitz, C.; Tampé, R.: Antigenic Peptide Recognition on the Human ABC Transporter TAP Resolved by DNP-Enhanced Solid-State NMR Spectroscopy. Journal of the American Chemical Society 138 (42), pp. 13967 - 13974 (2016)

MPG.PuRe