Publikationen von Gerhard Hummer
Alle Typen
Zeitschriftenartikel (358)
1.
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15, 3992 (2024)
High-confidence 3D template matching for cryo-electron tomography. Nature Communications 2.
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10 (17), eadk6285 (2024)
Thinner is not always better: Optimizing cryo-lamellae for subtomogram averaging. Science Advances 3.
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63, e202402498 (2024)
Structure and internal dynamics of short RNA duplexes determined by a combination of pulsed EPR methods and MD simulations. Angewandte Chemie, International Edition in English 4.
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160, 114111 (2024)
Encoding prior knowledge in ensemble refinement. The Journal of Chemical Physics 5.
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Structure and assembly of a bacterial gasdermin pore. Nature (2024)
6.
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IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. Journal of Molecular Biology, 168546 (2024)
7.
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121 (11), e2314199121 (2024)
Mechanism of proton-powered c-ring rotation in a mitochondrial ATP synthase. PNAS 8.
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187 (5), S. 1296 - 1311.e26 (2024)
Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries. Cell 9.
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121 (9), e2318046121 (2024)
Mechanism and cellular function of direct membrane binding by the ESCRT and ERES-associated Ca2+-sensor ALG-2. Proceedings of the National Academy of Sciences of the United States of America 10.
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7 (2), S. 528 - 534 (2024)
Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly. ACS applied bio materials 11.
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Hierarchical Assembly of Single-Stranded RNA. Journal of Chemical Theory and Computation (2024)
12.
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10 (6), eadj8027 (2024)
Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore. Science Advances 13.
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12, RP90174 (2024)
Tracing the substrate translocation mechanism in P-glycoprotein. eLife 14.
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19 (23), S. 8919 - 8929 (2023)
Neighbor List Artifacts in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 15.
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14 (1), 7197 (2023)
Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides. Nature Communications 16.
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30 (11), S. 1774 - 1785 (2023)
Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments. Nature Structural & Molecular Biology 17.
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19 (20), S. 7387 - 7404 (2023)
Martini 3 Coarse-Grained Force Field for Cholesterol. Journal of Chemical Theory and Computation 18.
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108 (3), 035307 (2023)
Efficient generation of random rotation matrices in four dimensions. Physical Review E 19.
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33 (16), S. 3423 - 3435.e5 (2023)
Structure-function analysis suggests that the photoreceptor LITE-1 is a light-activated ion channel. Current biology: CB 20.
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19 (8), S. 992 - 1003 (2023)
Dissecting the conformational complexity and mechanism of a bacterial heme transporter. Nature Chemical Biology 21.
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14, 4165 (2023)
Crosstalk between regulatory elements in disordered TRPV4 N-terminus modulates lipid-dependent channel activity. Nature Communications 22.
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19, S. 3406 - 3417 (2023)
Unwrapping NPT Simulations to Calculate Diffusion Coefficients. Journal of Chemical Theory and Computation 23.
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618 (7964), S. 402 - 410 (2023)
Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy. Nature 24.
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618 (7964), S. 394 - 401 (2023)
Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum. Nature 25.
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30 (5), S. 499 - 512 (2023)
Selective killing of the human gastric pathogen Helicobacter pylori by mitochondrial respiratory complex I inhibitors. Cell Chemical Biology 26.
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617 (7959), S. 162 - 169 (2023)
Visualizing the disordered nuclear transport machinery in situ. Nature 27.
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3 (4), S. 334 - 345 (2023)
Machine-guided path sampling to discover mechanisms of molecular self-organization. Nature Computational Science 28.
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19 (5), S. 1592 - 1601 (2023)
Optimal Bond Constraint Topology for Molecular Dynamics Simulations of Cholesterol. Journal of Chemical Theory and Computation 29.
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78, 102501 (2023)
Structural ensembles of disordered proteins from hierarchical chain growth and simulation. Current Opinion in Structural Biology 30.
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19 (1), e1010822 (2023)
Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants. PLoS Computational Biology 31.
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13 (1), 7926 (2022)
Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level. Nature Communications 32.
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8 (50), eadd1436 (2022)
Membrane curvature sensing and stabilization by the autophagic LC3 lipidation machinery. Science Advances 33.
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157 (20), 204802 (2022)
Complexes++: Efficient and versatile coarse-grained simulations of protein complexes and their dense solutions. The Journal of Chemical Physics 34.
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11, e81432 (2022)
Sublytic gasdermin-D pores captured in atomistic molecular simulations. eLife 35.
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157 (17), 174801 (2022)
TriMem: A parallelized hybrid Monte Carlo software for efficient simulations of lipid membranes. The Journal of Chemical Physics 36.
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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 37.
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41 (18), e109990 (2022)
Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism. The EMBO Journal 38.
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13 (32), S. 7490 - 7496 (2022)
Transition Rates and Efficiency of Collective Variables from Time-Dependent Biased Simulations. The Journal of Physical Chemistry Letters 39.
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185 (17), S. 3201 - 3213 (2022)
Structure of a fully assembled tumor-specific T cell receptor ligated by pMHC. Cell 40.
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4 (3), 033097 (2022)
Reversible bond kinetics from single-molecule force spectroscopy experiments close to equilibrium. Physical Review Research 41.
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157 (3), 034101 (2022)
Small ionic radii limit time step in Martini 3 molecular dynamics simulations. The Journal of Chemical Physics 42.
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376 (6598), eabm9506 (2022)
AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science 43.
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82 (11), S. 2006 - 2020.e8 (2022)
Kinase domain autophosphorylation rewires the activity and substrate specificity of CK1 enzymes. Molecular Cell 44.
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13, 1224 (2022)
Co-translational assembly orchestrates competing biogenesis pathways. Nature Communications 45.
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2 (3), S. 673 - 686 (2022)
Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure. JACS Au 46.
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13 (1), 1022 (2022)
Evidence for a trap-and-flip mechanism in a proton-dependent lipid transporter. Nature Communications 47.
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41 (3), e108443 (2022)
Disease-linked TDP-43 hyperphosphorylation suppresses TDP-43 condensation and aggregation. EMBO Journal 48.
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94 (12), 245 (2021)
Empirical optimization of molecular simulation force fields by Bayesian inference. The European Physical Journal B: Condensend Matter Physics 49.
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374 (6573), eabd9776 (2021)
Nuclear pores dilate and constrict in cellulo. Science 50.
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81, S. 4635 - 4649 (2021)
Structural basis of polyamine transport by human ATP13A2 (PARK9). Molecular Cell 51.
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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 52.
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1 (12), S. 2162 - 2171 (2021)
Solution Structure and Conformational Flexibility of a Polyketide Synthase Module. JACS Au 53.
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121 (19), S. 11701 - 11725 (2021)
Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems. Chemical Reviews 54.
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22 (9), e52289 (2021)
Role of FAM134 paralogues in endoplasmic reticulum remodeling, ER-phagy, and Collagen quality control. EMBO Reports 55.
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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 56.
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220 (8), e202011078 (2021)
Cysteine cross-linking in native membranes establishes the transmembrane architecture of Ire1. The Journal of Cell Biology 57.
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297 (2), 100925 (2021)
Famotidine inhibits Toll-like receptor 3-mediated inflammatory signaling in SARS-CoV2 infection. The Journal of Biological Chemistry 58.
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125 (28), S. 7732 - 7741 (2021)
Binding of SARS-CoV-2 Fusion Peptide to Host Endosome and Plasma Membrane. The Journal of Physical Chemistry B 59.
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154 (23), 234105 (2021)
Maximum likelihood estimates of diffusion coefficients from single-particle tracking experiments. The Journal of Chemical Physics 60.
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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 61.
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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 62.
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17 (4), e1008790 (2021)
Computational epitope map of SARS-CoV-2 spike protein. PLoS Computational Biology 63.
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12 (7), S. 1926 - 1931 (2021)
FAM134B-RHD Protein Clustering Drives Spontaneous Budding of Asymmetric Membranes. The Journal of Physical Chemistry Letters 64.
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17 (1), S. 525 - 537 (2021)
Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model. Journal of Chemical Theory and Computation 65.
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28 (1), S. 2 - 7 (2021)
Structural biology in the fight against COVID-19. Nature Structural and Molecular Biology 66.
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17 (1), S. 1 - 382 (2021)
Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy 67.
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59, S. 23025 - 23029 (2020)
Compaction of RNA duplexes in the cell. Angewandte Chemie, International Edition in English 68.
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587 (7835), S. 657 - 662 (2020)
Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature 69.
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9 (2020)
Bacterial OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection. eLife 70.
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117 (44), S. 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 71.
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370 (6513), S. 203 - 208 (2020)
In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. Science 72.
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16 (10), S. 1078 - 1086 (2020)
p63 uses a switch-like mechanism to set the threshold for induction of apoptosis. Nature Chemical Biology 73.
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153 (14), 144105 (2020)
MDBenchmark: A toolkit to optimize the performance of molecular dynamics simulations. The Journal of Chemical Physics 74.
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369 (6508), eaaz7714 (2020)
Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation. Science 75.
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4, 100032 (2020)
Validation tests for cryo-EM maps using an independent particle set. Journal of Structural Biology: X 76.
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153 (2), 024116 (2020)
Optimal estimates of self-diffusion coefficients from molecular dynamics simulations. The Journal of Chemical Physics 77.
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153 (2), 021101 (2020)
Systematic errors in diffusion coefficients from long-time molecular dynamics simulations at constant pressure. The Journal of Chemical Physics 78.
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124 (23), S. 4673 - 4685 (2020)
Quantifying Protein-Protein Interactions in Molecular Simulations. The Journal of Physical Chemistry B 79.
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368 (6489), eaaz2449, S. 385 (2020)
Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. Science 80.
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117 (10), S. 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 81.
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11, 756 (2020)
Regulation of lipid saturation without sensing membrane fluidity. Nature Communications 82.
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48 (2), S. 924 - 933 (2020)
High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label. Nucleic Acids Research 83.
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124 (2), S. 336 - 344 (2020)
Ion Binding and Selectivity of the Na+/H+ Antiporter MjNhaP1 from Experiment and Simulation. The Journal of Physical Chemistry B 84.
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16 (1), S. 725 - 737 (2020)
Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 85.
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77 (1), S. 164 - 179 (2020)
Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB. Molecular Cell 86.
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27 (12), S. 1745 - 1759 (2019)
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure 87.
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52 (47), 474002 (2019)
Molecule counts in complex oligomers with single-molecule localization microscopy. Journal of Physics D: Applied Physics 88.
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21 (1), e48317 (2019)
TBK1-mediated phosphorylation of LC3C and GABARAP-L2 controls autophagosome shedding by ATG4 protease. EMBO Reports 89.
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10 (20), S. 6351 - 6354 (2019)
Phospholipid Scramblases Remodel the Shape of Asymmetric Membranes. The Journal of Physical Chemistry Letters 90.
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151 (15), 154115 (2019)
Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors. The Journal of Chemical Physics 91.
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15 (9), S. 4974 - 4981 (2019)
Fragment Binding Pose Predictions Using Unbiased Simulations and Markov-State Models. Journal of Chemical Theory and Computation 92.
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75 (5), S. 1043 - 1057 (2019)
Osh Proteins Control Nanoscale Lipid Organization Necessary for PI(4,5)P2 Synthesis. Molecular Cell 93.
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571 (7766), S. 580 - 583 (2019)
Conformation space of a heterodimeric ABC exporter under turnover conditions. Nature 94.
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116 (27), S. 13352 - 13357 (2019)
Membrane perforation by the pore-forming toxin pneumolysin. Proceedings of the National Academy of Sciences of the United States of America 95.
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123 (24), S. 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 96.
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116 (25), S. 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 97.
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10, 2370 (2019)
Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy. Nature Communications 98.
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15 (5), S. 3390 - 3409 (2019)
Efficient Ensemble Refinement by Reweighting. Journal of Chemical Theory and Computation 99.
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116 (20), S. 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 100.
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10, 2032 (2019)
Structural basis for functional interactions in dimers of SLC26 transporters. Nature Communications