
Publications of Gerhard Hummer
All genres
Journal Article (315)
1.
Journal Article
82 (2022)
Kinase domain autophosphorylation rewires the activity and substrate specificity of CK1 enzymes. Molecular Cell 2.
Journal Article
13, 1224 (2022)
Co-translational assembly orchestrates competing biogenesis pathways. Nature Communications 3.
Journal Article
2 (3), pp. 673 - 686 (2022)
Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure. JACS Au 4.
Journal Article
13 (1), 1022 (2022)
Evidence for a trap-and-flip mechanism in a proton-dependent lipid transporter. Nature Communications 5.
Journal Article
41 (3), e108443 (2022)
Disease-linked TDP-43 hyperphosphorylation suppresses TDP-43 condensation and aggregation. EMBO Journal 6.
Journal Article
94 (12), 245 (2021)
Empirical optimization of molecular simulation force fields by Bayesian inference. The European Physical Journal B: Condensend Matter Physics 7.
Journal Article
374 (6573), eabd9776 (2021)
Nuclear pores dilate and constrict in cellulo. Science 8.
Journal Article
81, pp. 4635 - 4649 (2021)
Structural basis of polyamine transport by human ATP13A2 (PARK9). Molecular Cell 9.
Journal Article
118 (46), e2107335118 (2021)
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 10.
Journal Article
1 (12), pp. 2162 - 2171 (2021)
Solution Structure and Conformational Flexibility of a Polyketide Synthase Module. JACS Au 11.
Journal Article
121 (19), pp. 11701 - 11725 (2021)
Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems. Chemical Reviews 12.
Journal Article
22 (9), e52289 (2021)
Role of FAM134 paralogues in endoplasmic reticulum remodeling, ER-phagy, and Collagen quality control. EMBO Reports 13.
Journal Article
12 (1), 5236 (2021)
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 14.
Journal Article
220 (8), e202011078 (2021)
Cysteine cross-linking in native membranes establishes the transmembrane architecture of Ire1. The Journal of Cell Biology 15.
Journal Article
297 (2), 100925 (2021)
Famotidine inhibits Toll-like receptor 3-mediated inflammatory signaling in SARS-CoV2 infection. The Journal of Biological Chemistry 16.
Journal Article
125 (28), pp. 7732 - 7741 (2021)
Binding of SARS-CoV-2 Fusion Peptide to Host Endosome and Plasma Membrane. The Journal of Physical Chemistry B 17.
Journal Article
154 (23), 234105 (2021)
Maximum likelihood estimates of diffusion coefficients from single-particle tracking experiments. The Journal of Chemical Physics 18.
Journal Article
118 (19), e2100425118 (2021)
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 19.
Journal Article
118 (19), e2016974118 (2021)
Membrane fusion and drug delivery with carbon nanotube porins. Proceedings of the National Academy of Sciences of the United States of America 20.
Journal Article
17 (4), e1008790 (2021)
Computational epitope map of SARS-CoV-2 spike protein. PLoS Computational Biology 21.
Journal Article
12 (7), pp. 1926 - 1931 (2021)
FAM134B-RHD Protein Clustering Drives Spontaneous Budding of Asymmetric Membranes. The Journal of Physical Chemistry Letters 22.
Journal Article
17 (1), pp. 525 - 537 (2021)
Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model. Journal of Chemical Theory and Computation 23.
Journal Article
28 (1), pp. 2 - 7 (2021)
Structural biology in the fight against COVID-19. Nature Structural and Molecular Biology 24.
Journal Article
17 (1), pp. 1 - 382 (2021)
Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy 25.
Journal Article
59, pp. 23025 - 23029 (2020)
Compaction of RNA duplexes in the cell. Angewandte Chemie, International Edition in English 26.
Journal Article
587 (7835), pp. 657 - 662 (2020)
Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature 27.
Journal Article
9 (2020)
Bacterial OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection. eLife 28.
Journal Article
117 (44), pp. 27132 - 27140 (2020)
Desmosome architecture derived from molecular dynamics simulations and cryo-electron tomography. Proceedings of the National Academy of Sciences of the United States of America 29.
Journal Article
370 (6513), pp. 203 - 208 (2020)
In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. Science 30.
Journal Article
16 (10), pp. 1078 - 1086 (2020)
p63 uses a switch-like mechanism to set the threshold for induction of apoptosis. Nature Chemical Biology 31.
Journal Article
153 (14), 144105 (2020)
MDBenchmark: A toolkit to optimize the performance of molecular dynamics simulations. The Journal of Chemical Physics 32.
Journal Article
369 (6508), eaaz7714 (2020)
Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation. Science 33.
Journal Article
4, 100032 (2020)
Validation tests for cryo-EM maps using an independent particle set. Journal of Structural Biology: X 34.
Journal Article
153 (2), 024116 (2020)
Optimal estimates of self-diffusion coefficients from molecular dynamics simulations. The Journal of Chemical Physics 35.
Journal Article
153 (2), 021101 (2020)
Systematic errors in diffusion coefficients from long-time molecular dynamics simulations at constant pressure. The Journal of Chemical Physics 36.
Journal Article
124 (23), pp. 4673 - 4685 (2020)
Quantifying Protein-Protein Interactions in Molecular Simulations. The Journal of Physical Chemistry B 37.
Journal Article
368 (6489), eaaz2449, p. 385 (2020)
Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. Science 38.
Journal Article
117 (10), pp. 5109 - 5110 (2020)
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 39.
Journal Article
11, 756 (2020)
Regulation of lipid saturation without sensing membrane fluidity. Nature Communications 40.
Journal Article
48 (2), pp. 924 - 933 (2020)
High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label. Nucleic Acids Research 41.
Journal Article
124 (2), pp. 336 - 344 (2020)
Ion Binding and Selectivity of the Na+/H+ Antiporter MjNhaP1 from Experiment and Simulation. The Journal of Physical Chemistry B 42.
Journal Article
16 (1), pp. 725 - 737 (2020)
Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 43.
Journal Article
77 (1), pp. 164 - 179 (2020)
Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB. Molecular Cell 44.
Journal Article
27 (12), pp. 1745 - 1759 (2019)
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure 45.
Journal Article
52 (47), 474002 (2019)
Molecule counts in complex oligomers with single-molecule localization microscopy. Journal of Physics D: Applied Physics 46.
Journal Article
21 (1), e48317 (2019)
TBK1-mediated phosphorylation of LC3C and GABARAP-L2 controls autophagosome shedding by ATG4 protease. EMBO Reports 47.
Journal Article
151 (15), 154115 (2019)
Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors. The Journal of Chemical Physics 48.
Journal Article
15 (9), pp. 4974 - 4981 (2019)
Fragment Binding Pose Predictions Using Unbiased Simulations and Markov-State Models. Journal of Chemical Theory and Computation 49.
Journal Article
75 (5), pp. 1043 - 1057 (2019)
Osh Proteins Control Nanoscale Lipid Organization Necessary for PI(4,5)P2 Synthesis. Molecular Cell 50.
Journal Article
571 (7766), pp. 580 - 583 (2019)
Conformation space of a heterodimeric ABC exporter under turnover conditions. Nature 51.
Journal Article
116 (27), pp. 13352 - 13357 (2019)
Membrane perforation by the pore-forming toxin pneumolysin. Proceedings of the National Academy of Sciences of the United States of America 52.
Journal Article
123 (24), pp. 5099 - 5106 (2019)
Finite-Size-Corrected Rotational Diffusion Coefficients of Membrane Proteins and Carbon Nanotubes from Molecular Dynamics Simulations. The Journal of Physical Chemistry B 53.
Journal Article
116 (25), pp. 12275 - 12284 (2019)
Inward-facing conformation of a multidrug resistance MATE family transporter. Proceedings of the National Academy of Sciences of the United States of America 54.
Journal Article
10, 2370 (2019)
Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy. Nature Communications 55.
Journal Article
15 (5), pp. 3390 - 3409 (2019)
Efficient Ensemble Refinement by Reweighting. Journal of Chemical Theory and Computation 56.
Journal Article
116 (20), pp. 9843 - 9852 (2019)
Dynamic cluster formation determines viscosity and diffusion in dense protein solutions. Proceedings of the National Academy of Sciences of the United States of America 57.
Journal Article
10, 2032 (2019)
Structural basis for functional interactions in dimers of SLC26 transporters. Nature Communications 58.
Journal Article
10, 1742 (2019)
Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting. Nature Communications 59.
Journal Article
27 (4), pp. 669 - 678.e5 (2019)
Structure of Outward-Facing PglK and Molecular Dynamics of Lipid-Linked Oligosaccharide Recognition and Translocation. Structure 60.
Journal Article
123 (10), pp. 5989 - 5998 (2019)
Multifaceted Water Dynamics in Spherical Nanocages. The Journal of Physical Chemistry C 61.
Journal Article
73 (2), pp. 339 - 353 (2019)
Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics. Molecular Cell 62.
Journal Article
10884, 108840T (2019)
Quantification of membrane receptor complexes with single-molecule localization microscopy. Proceedings of SPIE 63.
Journal Article
362 (6421), pp. 1423 - 1428 (2018)
ATP-dependent force generation and membrane scission by ESCRT-III and Vps4. Science 64.
Journal Article
122 (49), pp. 11626 - 11639 (2018)
Dispersion Correction Alleviates Dye Stacking of Single-Stranded DNA and RNA in Simulations of Single-Molecule Fluorescence Experiments. The Journal of Physical Chemistry B 65.
Journal Article
24 (66), pp. 17568 - 17576 (2018)
Optimal Destabilization of DNA Double Strands by Single-Nucleobase Caging. Chemistry – A European Journal 66.
Journal Article
8, 15662 (2018)
Structural and functional insights into the interaction and targeting hub TMD0 of the polypeptide transporter TAPL. Scientific Reports 67.
Journal Article
54 (82), pp. 11606 - 11609 (2018)
Analysis and engineering of substrate shuttling by the acyl carrier protein (ACP) in fatty acid synthases (FASs). Chemical Communications 68.
Journal Article
9 (18), pp. 5748 - 5752 (2018)
Precision DEER Distances from Spin-Label Ensemble Refinement. The Journal of Physical Chemistry Letters 69.
Journal Article
67 (5), pp. 266 - 273 (2018)
Bayesian inference of rotor ring stoichiometry from electron microscopy images of archaeal ATP synthase. Microscopy 70.
Journal Article
115 (36), pp. E8413 - E8420 (2018)
Redox-coupled quinone dynamics in the respiratory complex I. Proceedings of the National Academy of Sciences of the United States of America 71.
Journal Article
217 (9), pp. 3109 - 3126 (2018)
The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1. The Journal of Cell Biology: JCB 72.
Journal Article
209, pp. 341 - 358 (2018)
Molecular dynamics simulations of carbon nanotube porins in lipid bilayers. Faraday Discussions 73.
Journal Article
71 (3), pp. 458 - 467 (2018)
Integrated Functions of Membrane Property Sensors and a Hidden Side of the Unfolded Protein Response. Molecular Cell 74.
Journal Article
120 (26), 268104 (2018)
Hydrodynamics of Diffusion in Lipid Membrane Simulations. Physical Review Letters 75.
Journal Article
14 (7), pp. 3811 - 3824 (2018)
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 76.
Journal Article
9 (11), pp. 2874 - 2878 (2018)
Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations. The Journal of Physical Chemistry Letters 77.
Journal Article
122 (21), pp. 5630 - 5639 (2018)
Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations. The Journal of Physical Chemistry B 78.
Journal Article
115 (14), pp. 3557 - 3562 (2018)
Retinal isomerization and water-pore formation in channelrhodopsin-2. Proceedings of the National Academy of Sciences of the United States of America 79.
Journal Article
49, pp. 162 - 168 (2018)
Likelihood-based structural analysis of electron microscopy images. Current Opinion in Structural Biology 80.
Journal Article
148 (12), 123309 (2018)
Transition paths in single-molecule force spectroscopy. The Journal of Chemical Physics 81.
Journal Article
9, 445 (2018)
Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase. Nature Communications 82.
Journal Article
6, 10.7554/eLife.30483 (2017)
Cryo-EM structure of the bifunctional secretin complex of Thermus thermophilus. eLife 83.
Journal Article
13 (12), pp. 6328 - 6342 (2017)
Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations. Journal of Chemical Theory and Computation 84.
Journal Article
57 (11), pp. 2833 - 2845 (2017)
Classical Molecular Dynamics with Mobile Protons. Journal of Chemical Information and Modeling 85.
Journal Article
13 (10), e1005817 (2017)
Scaffolding the cup-shaped double membrane in autophagy. PLoS Computational Biology 86.
Journal Article
147 (15), 152716 (2017)
Transition path sampling of rare events by shooting from the top. The Journal of Chemical Physics 87.
Journal Article
147 (15), 152725 (2017)
Peptide dimerization-dissociation rates from replica exchange molecular dynamics. The Journal of Chemical Physics 88.
Journal Article
7 (3), 031060 (2017)
Variational Identification of Markovian Transition States. Physical Review X 89.
Journal Article
11 (9), pp. 9558 - 9565 (2017)
Formation and Stability of Lipid Membrane Nanotubes. ACS Nano 90.
Journal Article
112 (37), pp. 11571 - 11576 (2017)
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 91.
Journal Article
139 (34), pp. 11674 - 11677 (2017)
Resolving the Conformational Dynamics of DNA with Ångstrom Resolution by Pulsed Electron–Electron Double Resonance and Molecular Dynamics. Journal of the American Chemical Society 92.
Journal Article
67 (4), pp. 673 - 684 (2017)
Activation of the Unfolded Protein Response by Lipid Bilayer Stress. Molecular Cell 93.
Journal Article
13 (8), pp. 3927 - 3935 (2017)
Kinetics from Replica Exchange Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 94.
Journal Article
114 (28), pp. E5494 - E5503 (2017)
Intrinsic map dynamics exploration for uncharted effective free-energy landscapes. Proceedings of the National Academy of Sciences of the United States of America 95.
Journal Article
6, e23471 (2017)
Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and coevolutionary sequence analysis. eLife 96.
Journal Article
13 (6), pp. 2962 - 2976 (2017)
Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes. Journal of Chemical Theory and Computation 97.
Journal Article
85 (5), pp. 812 - 826 (2017)
Systematic evaluation of CS‐Rosetta for membrane protein structure prediction with sparse NOE restraints. Proteins: Structure, Function, and Bioinformatics 98.
Journal Article
121 (15), pp. 3331 - 3339 (2017)
Dynamics of the Orientational Factor in Fluorescence Resonance Energy Transfer. The Journal of Physical Chemistry B 99.
Journal Article
18 (8), pp. 942 - 948 (2017)
Molecule Counts in Localization Microscopy with Organic Fluorophores. ChemPhysChem 100.
Journal Article
11 (2), pp. 1273 - 1280 (2017)
Carbon Nanotubes Mediate Fusion of Lipid Vesicles. ACS Nano