
Publications of Gerhard Hummer
All genres
Journal Article (339)
1.
Journal Article
Unwrapping NPT Simulations to Calculate Diffusion Coefficients. Journal of Chemical Theory and Computation (2023)
2.
Journal Article
Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy. Nature (2023)
3.
Journal Article
Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum. Nature, pp. 1 - 8 (2023)
4.
Journal Article
30 (5), pp. 499 - 512 (2023)
Selective killing of the human gastric pathogen Helicobacter pylori by mitochondrial respiratory complex I inhibitors. Cell Chemical Biology 5.
Journal Article
Visualizing the disordered nuclear transport machinery in situ. Nature (2023)
6.
Journal Article
3 (4), pp. 334 - 345 (2023)
Machine-guided path sampling to discover mechanisms of molecular self-organization. Nature Computational Science 7.
Journal Article
10, pp. 1 - 12 (2023)
Dissecting the conformational complexity and mechanism of a bacterial heme transporter. Nature Chemical Biology 8.
Journal Article
19 (5), pp. 1592 - 1601 (2023)
Optimal Bond Constraint Topology for Molecular Dynamics Simulations of Cholesterol. Journal of Chemical Theory and Computation 9.
Journal Article
78, 102501 (2023)
Structural ensembles of disordered proteins from hierarchical chain growth and simulation. Current Opinion in Structural Biology 10.
Journal Article
19 (1), e1010822 (2023)
Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants. PLoS Computational Biology 11.
Journal Article
13 (1), 7926 (2022)
Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level. Nature Communications 12.
Journal Article
8 (50), eadd1436 (2022)
Membrane curvature sensing and stabilization by the autophagic LC3 lipidation machinery. Science Advances 13.
Journal Article
157 (20), 204802 (2022)
Complexes++: Efficient and versatile coarse-grained simulations of protein complexes and their dense solutions. The Journal of Chemical Physics 14.
Journal Article
11, e81432 (2022)
Sublytic gasdermin-D pores captured in atomistic molecular simulations. eLife 15.
Journal Article
157 (17), 174801 (2022)
TriMem: A parallelized hybrid Monte Carlo software for efficient simulations of lipid membranes. The Journal of Chemical Physics 16.
Journal Article
119 (39), e2209823119 (2022)
In situ structural analysis reveals membrane shape transitions during autophagosome formation. Proceedings of the National Academy of Sciences of the United States of America 17.
Journal Article
41 (18), e109990 (2022)
Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism. The EMBO Journal 18.
Journal Article
Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly. ACS applied bio materials (2022)
19.
Journal Article
13 (32), pp. 7490 - 7496 (2022)
Transition Rates and Efficiency of Collective Variables from Time-Dependent Biased Simulations. The Journal of Physical Chemistry Letters 20.
Journal Article
185 (17), pp. 3201 - 3213 (2022)
Structure of a fully assembled tumor-specific T cell receptor ligated by pMHC. Cell 21.
Journal Article
4 (3), 033097 (2022)
Reversible bond kinetics from single-molecule force spectroscopy experiments close to equilibrium. Physical Review Research 22.
Journal Article
157 (3), 034101 (2022)
Small ionic radii limit time step in Martini 3 molecular dynamics simulations. The Journal of Chemical Physics 23.
Journal Article
376 (6598), eabm9506 (2022)
AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science 24.
Journal Article
82 (11), pp. 2006 - 2020.e8 (2022)
Kinase domain autophosphorylation rewires the activity and substrate specificity of CK1 enzymes. Molecular Cell 25.
Journal Article
13, 1224 (2022)
Co-translational assembly orchestrates competing biogenesis pathways. Nature Communications 26.
Journal Article
2 (3), pp. 673 - 686 (2022)
Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure. JACS Au 27.
Journal Article
13 (1), 1022 (2022)
Evidence for a trap-and-flip mechanism in a proton-dependent lipid transporter. Nature Communications 28.
Journal Article
41 (3), e108443 (2022)
Disease-linked TDP-43 hyperphosphorylation suppresses TDP-43 condensation and aggregation. EMBO Journal 29.
Journal Article
94 (12), 245 (2021)
Empirical optimization of molecular simulation force fields by Bayesian inference. The European Physical Journal B: Condensend Matter Physics 30.
Journal Article
374 (6573), eabd9776 (2021)
Nuclear pores dilate and constrict in cellulo. Science 31.
Journal Article
81, pp. 4635 - 4649 (2021)
Structural basis of polyamine transport by human ATP13A2 (PARK9). Molecular Cell 32.
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 33.
Journal Article
1 (12), pp. 2162 - 2171 (2021)
Solution Structure and Conformational Flexibility of a Polyketide Synthase Module. JACS Au 34.
Journal Article
121 (19), pp. 11701 - 11725 (2021)
Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems. Chemical Reviews 35.
Journal Article
22 (9), e52289 (2021)
Role of FAM134 paralogues in endoplasmic reticulum remodeling, ER-phagy, and Collagen quality control. EMBO Reports 36.
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 37.
Journal Article
220 (8), e202011078 (2021)
Cysteine cross-linking in native membranes establishes the transmembrane architecture of Ire1. The Journal of Cell Biology 38.
Journal Article
297 (2), 100925 (2021)
Famotidine inhibits Toll-like receptor 3-mediated inflammatory signaling in SARS-CoV2 infection. The Journal of Biological Chemistry 39.
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 40.
Journal Article
154 (23), 234105 (2021)
Maximum likelihood estimates of diffusion coefficients from single-particle tracking experiments. The Journal of Chemical Physics 41.
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 42.
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 43.
Journal Article
17 (4), e1008790 (2021)
Computational epitope map of SARS-CoV-2 spike protein. PLoS Computational Biology 44.
Journal Article
12 (7), pp. 1926 - 1931 (2021)
FAM134B-RHD Protein Clustering Drives Spontaneous Budding of Asymmetric Membranes. The Journal of Physical Chemistry Letters 45.
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 46.
Journal Article
28 (1), pp. 2 - 7 (2021)
Structural biology in the fight against COVID-19. Nature Structural and Molecular Biology 47.
Journal Article
17 (1), pp. 1 - 382 (2021)
Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy 48.
Journal Article
59, pp. 23025 - 23029 (2020)
Compaction of RNA duplexes in the cell. Angewandte Chemie, International Edition in English 49.
Journal Article
587 (7835), pp. 657 - 662 (2020)
Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature 50.
Journal Article
9 (2020)
Bacterial OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection. eLife 51.
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 52.
Journal Article
370 (6513), pp. 203 - 208 (2020)
In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. Science 53.
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 54.
Journal Article
153 (14), 144105 (2020)
MDBenchmark: A toolkit to optimize the performance of molecular dynamics simulations. The Journal of Chemical Physics 55.
Journal Article
369 (6508), eaaz7714 (2020)
Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation. Science 56.
Journal Article
4, 100032 (2020)
Validation tests for cryo-EM maps using an independent particle set. Journal of Structural Biology: X 57.
Journal Article
153 (2), 024116 (2020)
Optimal estimates of self-diffusion coefficients from molecular dynamics simulations. The Journal of Chemical Physics 58.
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 59.
Journal Article
124 (23), pp. 4673 - 4685 (2020)
Quantifying Protein-Protein Interactions in Molecular Simulations. The Journal of Physical Chemistry B 60.
Journal Article
368 (6489), eaaz2449, p. 385 (2020)
Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. Science 61.
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 62.
Journal Article
11, 756 (2020)
Regulation of lipid saturation without sensing membrane fluidity. Nature Communications 63.
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 64.
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 65.
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 66.
Journal Article
77 (1), pp. 164 - 179 (2020)
Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB. Molecular Cell 67.
Journal Article
27 (12), pp. 1745 - 1759 (2019)
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure 68.
Journal Article
52 (47), 474002 (2019)
Molecule counts in complex oligomers with single-molecule localization microscopy. Journal of Physics D: Applied Physics 69.
Journal Article
21 (1), e48317 (2019)
TBK1-mediated phosphorylation of LC3C and GABARAP-L2 controls autophagosome shedding by ATG4 protease. EMBO Reports 70.
Journal Article
10 (20), pp. 6351 - 6354 (2019)
Phospholipid Scramblases Remodel the Shape of Asymmetric Membranes. The Journal of Physical Chemistry Letters 71.
Journal Article
151 (15), 154115 (2019)
Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors. The Journal of Chemical Physics 72.
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 73.
Journal Article
75 (5), pp. 1043 - 1057 (2019)
Osh Proteins Control Nanoscale Lipid Organization Necessary for PI(4,5)P2 Synthesis. Molecular Cell 74.
Journal Article
571 (7766), pp. 580 - 583 (2019)
Conformation space of a heterodimeric ABC exporter under turnover conditions. Nature 75.
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 76.
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 77.
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 78.
Journal Article
10, 2370 (2019)
Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy. Nature Communications 79.
Journal Article
15 (5), pp. 3390 - 3409 (2019)
Efficient Ensemble Refinement by Reweighting. Journal of Chemical Theory and Computation 80.
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 81.
Journal Article
10, 2032 (2019)
Structural basis for functional interactions in dimers of SLC26 transporters. Nature Communications 82.
Journal Article
10, 1742 (2019)
Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting. Nature Communications 83.
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 84.
Journal Article
123 (10), pp. 5989 - 5998 (2019)
Multifaceted Water Dynamics in Spherical Nanocages. The Journal of Physical Chemistry C 85.
Journal Article
73 (2), pp. 339 - 353 (2019)
Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics. Molecular Cell 86.
Journal Article
10884, 108840T (2019)
Quantification of membrane receptor complexes with single-molecule localization microscopy. Proceedings of SPIE 87.
Journal Article
362 (6421), pp. 1423 - 1428 (2018)
ATP-dependent force generation and membrane scission by ESCRT-III and Vps4. Science 88.
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 89.
Journal Article
24 (66), pp. 17568 - 17576 (2018)
Optimal Destabilization of DNA Double Strands by Single-Nucleobase Caging. Chemistry – A European Journal 90.
Journal Article
8, 15662 (2018)
Structural and functional insights into the interaction and targeting hub TMD0 of the polypeptide transporter TAPL. Scientific Reports 91.
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 92.
Journal Article
9 (18), pp. 5748 - 5752 (2018)
Precision DEER Distances from Spin-Label Ensemble Refinement. The Journal of Physical Chemistry Letters 93.
Journal Article
67 (5), pp. 266 - 273 (2018)
Bayesian inference of rotor ring stoichiometry from electron microscopy images of archaeal ATP synthase. Microscopy 94.
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 95.
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 96.
Journal Article
209, pp. 341 - 358 (2018)
Molecular dynamics simulations of carbon nanotube porins in lipid bilayers. Faraday Discussions 97.
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 98.
Journal Article
120 (26), 268104 (2018)
Hydrodynamics of Diffusion in Lipid Membrane Simulations. Physical Review Letters 99.
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 100.
Journal Article
9 (11), pp. 2874 - 2878 (2018)
Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations. The Journal of Physical Chemistry Letters