Publikationen von Gerhard Hummer
Alle Typen
Zeitschriftenartikel (372)
2019
Zeitschriftenartikel
Molecule counts in complex oligomers with single-molecule localization microscopy. Journal of Physics D: Applied Physics 52 (47), 474002 (2019)
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TBK1-mediated phosphorylation of LC3C and GABARAP-L2 controls autophagosome shedding by ATG4 protease. EMBO Reports 21 (1), e48317 (2019)
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Phospholipid Scramblases Remodel the Shape of Asymmetric Membranes. The Journal of Physical Chemistry Letters 10 (20), S. 6351 - 6354 (2019)
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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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Fragment Binding Pose Predictions Using Unbiased Simulations and Markov-State Models. Journal of Chemical Theory and Computation 15 (9), S. 4974 - 4981 (2019)
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Osh Proteins Control Nanoscale Lipid Organization Necessary for PI(4,5)P2 Synthesis. Molecular Cell 75 (5), S. 1043 - 1057 (2019)
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Conformation space of a heterodimeric ABC exporter under turnover conditions. Nature 571 (7766), S. 580 - 583 (2019)
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Membrane perforation by the pore-forming toxin pneumolysin. Proceedings of the National Academy of Sciences of the United States of America 116 (27), S. 13352 - 13357 (2019)
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Finite-Size-Corrected Rotational Diffusion Coefficients of Membrane Proteins and Carbon Nanotubes from Molecular Dynamics Simulations. The Journal of Physical Chemistry B 123 (24), S. 5099 - 5106 (2019)
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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), S. 12275 - 12284 (2019)
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Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy. Nature Communications 10, 2370 (2019)
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Efficient Ensemble Refinement by Reweighting. Journal of Chemical Theory and Computation 15 (5), S. 3390 - 3409 (2019)
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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), S. 9843 - 9852 (2019)
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Structural basis for functional interactions in dimers of SLC26 transporters. Nature Communications 10, 2032 (2019)
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Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting. Nature Communications 10, 1742 (2019)
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Structure of Outward-Facing PglK and Molecular Dynamics of Lipid-Linked Oligosaccharide Recognition and Translocation. Structure 27 (4), S. 669 - 678.e5 (2019)
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Multifaceted Water Dynamics in Spherical Nanocages. The Journal of Physical Chemistry C 123 (10), S. 5989 - 5998 (2019)
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Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics. Molecular Cell 73 (2), S. 339 - 353 (2019)
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Quantification of membrane receptor complexes with single-molecule localization microscopy. Proceedings of SPIE 10884, 108840T (2019)
2018
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ATP-dependent force generation and membrane scission by ESCRT-III and Vps4. Science 362 (6421), S. 1423 - 1428 (2018)
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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), S. 11626 - 11639 (2018)
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Optimal Destabilization of DNA Double Strands by Single-Nucleobase Caging. Chemistry – A European Journal 24 (66), S. 17568 - 17576 (2018)
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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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Analysis and engineering of substrate shuttling by the acyl carrier protein (ACP) in fatty acid synthases (FASs). Chemical Communications 54 (82), S. 11606 - 11609 (2018)
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Precision DEER Distances from Spin-Label Ensemble Refinement. The Journal of Physical Chemistry Letters 9 (18), S. 5748 - 5752 (2018)
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Bayesian inference of rotor ring stoichiometry from electron microscopy images of archaeal ATP synthase. Microscopy 67 (5), S. 266 - 273 (2018)
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Redox-coupled quinone dynamics in the respiratory complex I. Proceedings of the National Academy of Sciences of the United States of America 115 (36), S. E8413 - E8420 (2018)
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The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1. The Journal of Cell Biology: JCB 217 (9), S. 3109 - 3126 (2018)
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Molecular dynamics simulations of carbon nanotube porins in lipid bilayers. Faraday Discussions 209, S. 341 - 358 (2018)
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Integrated Functions of Membrane Property Sensors and a Hidden Side of the Unfolded Protein Response. Molecular Cell 71 (3), S. 458 - 467 (2018)
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Hydrodynamics of Diffusion in Lipid Membrane Simulations. Physical Review Letters 120 (26), 268104 (2018)
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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), S. 3811 - 3824 (2018)
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Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations. The Journal of Physical Chemistry Letters 9 (11), S. 2874 - 2878 (2018)
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Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations. The Journal of Physical Chemistry B 122 (21), S. 5630 - 5639 (2018)
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Retinal isomerization and water-pore formation in channelrhodopsin-2. Proceedings of the National Academy of Sciences of the United States of America 115 (14), S. 3557 - 3562 (2018)
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Likelihood-based structural analysis of electron microscopy images. Current Opinion in Structural Biology 49, S. 162 - 168 (2018)
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Transition paths in single-molecule force spectroscopy. The Journal of Chemical Physics 148 (12), 123309 (2018)
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Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase. Nature Communications 9, 445 (2018)
2017
Zeitschriftenartikel
Cryo-EM structure of the bifunctional secretin complex of Thermus thermophilus. eLife 6, 10.7554/eLife.30483 (2017)
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Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations. Journal of Chemical Theory and Computation 13 (12), S. 6328 - 6342 (2017)
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Classical Molecular Dynamics with Mobile Protons. Journal of Chemical Information and Modeling 57 (11), S. 2833 - 2845 (2017)
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Scaffolding the cup-shaped double membrane in autophagy. PLoS Computational Biology 13 (10), e1005817 (2017)
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Transition path sampling of rare events by shooting from the top. The Journal of Chemical Physics 147 (15), 152716 (2017)
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Peptide dimerization-dissociation rates from replica exchange molecular dynamics. The Journal of Chemical Physics 147 (15), 152725 (2017)
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Variational Identification of Markovian Transition States. Physical Review X 7 (3), 031060 (2017)
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Formation and Stability of Lipid Membrane Nanotubes. ACS Nano 11 (9), S. 9558 - 9565 (2017)
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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), S. 11571 - 11576 (2017)
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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), S. 11674 - 11677 (2017)
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Activation of the Unfolded Protein Response by Lipid Bilayer Stress. Molecular Cell 67 (4), S. 673 - 684 (2017)
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Kinetics from Replica Exchange Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 13 (8), S. 3927 - 3935 (2017)
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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), S. E5494 - E5503 (2017)
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Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and coevolutionary sequence analysis. eLife 6, e23471 (2017)
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Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes. Journal of Chemical Theory and Computation 13 (6), S. 2962 - 2976 (2017)
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Systematic evaluation of CS‐Rosetta for membrane protein structure prediction with sparse NOE restraints. Proteins: Structure, Function, and Bioinformatics 85 (5), S. 812 - 826 (2017)
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Dynamics of the Orientational Factor in Fluorescence Resonance Energy Transfer. The Journal of Physical Chemistry B 121 (15), S. 3331 - 3339 (2017)
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Molecule Counts in Localization Microscopy with Organic Fluorophores. ChemPhysChem 18 (8), S. 942 - 948 (2017)
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Carbon Nanotubes Mediate Fusion of Lipid Vesicles. ACS Nano 11 (2), S. 1273 - 1280 (2017)
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Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies. The Journal of Physical Chemistry A 121 (7), S. 1525 - 1530 (2017)
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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), S. E438 - E447 (2017)
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BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images. Computer Physics Communications 210 (01), S. 163 - 171 (2017)
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Helical jackknives control the gates of the double-pore K+ uptake system KtrABs. eLife, S. 1 - 21 (2017)
2016
Zeitschriftenartikel
Model-independent counting of molecules in single-molecule localization microscopy. Molecular Biology of the Cell 27 (22), S. 3637 - 3644 (2016)
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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), S. 13967 - 13974 (2016)
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Divergent Diffusion Coefficients in Simulations of Fluids and Lipid Membranes. The Journal of Physical Chemistry B 25 (33), S. 8722 - 8732 (2016)
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Kinetic Ductility and Force-Spike Resistance of Proteins from Single-Molecule Force Spectroscopy. Biophysical Journal 111 (4), S. 832 - 840 (2016)
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Cardiolipin puts the seal on ATP synthase. Proceedings of the National Academy of Sciences of the United States of America 113 (31), S. 8568 - 8570 (2016)
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Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers. The Journal of Physical Chemistry Letters 7 (14), S. 2676 - 2682 (2016)
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A Eukaryotic Sensor for Membrane Lipid Saturation. Molecular Cell 63 (1), S. 49 - 59 (2016)
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Molecular simulation and modeling of complex I. Biochimica et Biophysica Acta, Bioenergetics 1857 (7), S. 915 - 921 (2016)
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F1-ATPase conformational cycle from simultaneous single-molecule FRET and rotation measurements. Proceedings of the National Academy of Sciences of the United States of America 113 (21), S. E2916 - E2924 (2016)
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Microscopic interpretation of folding ϕ-values using the transition path ensemble. Proceedings of the National Academy of Sciences of the United States of America 113 (12), S. 3263 - 3268 (2016)
2015
Zeitschriftenartikel
Bayesian ensemble refinement by replica simulations and reweighting. The Journal of Chemical Physics 143 (24), S. 243150-1 - 243150-14 (2015)
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Assembly of the MHC I peptideloading complex determined by a conserved ionic lock-switch. Scientific Reports 5, 17341 (2015)
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On artifacts in single-molecule force spectroscopy. Proceedings of the National Academy of Sciences of the United States of America 112 (46), S. 14248 - 14253 (2015)
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Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation. Science 350 (6259), S. 445 - 450 (2015)
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MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data. Journal of Biomolecular NMR 63 (1), S. 85 - 95 (2015)
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Elasticity, friction, and pathway of γ-subunit rotation in FoF1-ATP synthase. Proceedings of the National Academy of Sciences of the United States of America 112 (34), S. 10720 - 10725 (2015)
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Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models. The Journal of Physical Chemistry B 119 (29), S. 9029 - 9037 (2015)
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Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure 23 (7), S. 1156 - 1167 (2015)
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Accessory NUMM (NDUFS6) subunit harbors a Zn-binding site and is essential for biogenesis of mitochondrial complex I. Proceedings of the National Academy of Sciences of the United States of America 112 (18), S. 5685 - 5690 (2015)
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Solution Structure of the Atg1 Complex: Implications for the Architecture of the Phagophore Assembly Site. Structure 23 (5), S. 809 - 818 (2015)
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New Perspectives on Proton Pumping in Cellular Respiration. Chemical Reviews 115 (5), S. 2045 - 2222 (2015)
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Linear Energy Relationships in Ground State Proton Transfer and Excited State Proton-Coupled Electron Transfer. The Journal of Physical Chemistry B 119 (6), S. 2611 - 2619 (2015)
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Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model. Journal of Chemical Theory and Computation 11 (1), S. 276 - 285 (2015)
2014
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Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions. The Journal of Chemical Physics 141 (11), S. 114102 - 114117 (2014)
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Potassium ions line up. Do K+ ions move in single file through potassium channels? Science Magazine 346 (6207), S. 303 - 303 (2014)
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Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems. Physical Review X 4 (3), S. 031037 - 031058 (2014)
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A maximum entropy approach to the study of residue-specific backbone angle distributions in α-synuclein, an intrinsically disordered protein. Protein Science 23 (9), S. 1275 - 1290 (2014)
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Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I. Proceedings of the National Academy of Sciences of the United States of America 111 (19), S. 6988 - 6993 (2014)
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Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein. Nature Chemistry 6 (4), S. 258 - 259 (2014)
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Calcium Inhibition of Ribonuclease H1 Two-Metal Ion Catalysis. Journal of the American Chemical Society 136 (8), S. 3137 - 3144 (2014)
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Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics. Entropy 16 (1), S. 41 - 61 (2014)
2013
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Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies. Journal of Structural Biology 184 (3), S. 427 - 437 (2013)
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Native contacts determine protein folding mechanisms in atomistic simulations. Proceedings of the National Academy of Sciences of the United States of America 110 (44), S. 17874 - 17879 (2013)
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Evolutionary pressure on the topology of protein interface interaction networks. The Journal of Physical Chemistry B 117 (42), S. 13098 - 13106 (2013)
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Phosphate release coupled to rotary motion of F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America 110 (41), S. 16468 - 16473 (2013)
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Interface-resolved network of protein-protein interactions. PLoS Computational Biology 9 (5), e1003065 (2013)
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Atomic-resolution structural information from scattering experiments on macromolecules in solution. Physical Review E 87, 052712 (2013)
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The molecular mechanism of substrate engagement and immunosuppressant inhibition of calcineurin. PLoS Biology 11 (2), e1001492 (2013)
2012
Zeitschriftenartikel
Theoretical study of the mechanism of the hydride transfer between ferredoxin-NADP+ reductase and NADP+: the role of Tyr303. Journal of the American Chemical Society 134 (50), S. 20544 - 20553 (2012)