Publications of Gerhard Hummer
All genres
Journal Article (317)
101.
Journal Article
18 (8), pp. 942 - 948 (2017)
Molecule Counts in Localization Microscopy with Organic Fluorophores. ChemPhysChem 102.
Journal Article
11 (2), pp. 1273 - 1280 (2017)
Carbon Nanotubes Mediate Fusion of Lipid Vesicles. ACS Nano 103.
Journal Article
121 (7), pp. 1525 - 1530 (2017)
Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies. The Journal of Physical Chemistry A 104.
Journal Article
114 (4), pp. E438 - E447 (2017)
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 105.
Journal Article
210 (01), pp. 163 - 171 (2017)
BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images. Computer Physics Communications 106.
Journal Article
Helical jackknives control the gates of the double-pore K+ uptake system KtrABs. eLife, pp. 1 - 21 (2017)
107.
Journal Article
27 (22), pp. 3637 - 3644 (2016)
Model-independent counting of molecules in single-molecule localization microscopy. Molecular Biology of the Cell 108.
Journal Article
138 (42), pp. 13967 - 13974 (2016)
Antigenic Peptide Recognition on the Human ABC Transporter TAP Resolved by DNP-Enhanced Solid-State NMR Spectroscopy. Journal of the American Chemical Society 109.
Journal Article
25 (33), pp. 8722 - 8732 (2016)
Divergent Diffusion Coefficients in Simulations of Fluids and Lipid Membranes. The Journal of Physical Chemistry B 110.
Journal Article
111 (4), pp. 832 - 840 (2016)
Kinetic Ductility and Force-Spike Resistance of Proteins from Single-Molecule Force Spectroscopy. Biophysical Journal 111.
Journal Article
113 (31), pp. 8568 - 8570 (2016)
Cardiolipin puts the seal on ATP synthase. Proceedings of the National Academy of Sciences of the United States of America 112.
Journal Article
7 (14), pp. 2676 - 2682 (2016)
Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers. The Journal of Physical Chemistry Letters 113.
Journal Article
63 (1), pp. 49 - 59 (2016)
A Eukaryotic Sensor for Membrane Lipid Saturation. Molecular Cell 114.
Journal Article
1857 (7), pp. 915 - 921 (2016)
Molecular simulation and modeling of complex I. Biochimica et Biophysica Acta, Bioenergetics 115.
Journal Article
113 (21), pp. E2916 - E2924 (2016)
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 116.
Journal Article
113 (12), pp. 3263 - 3268 (2016)
Microscopic interpretation of folding ϕ-values using the transition path ensemble. Proceedings of the National Academy of Sciences of the United States of America 117.
Journal Article
143 (24), pp. 243150-1 - 243150-14 (2015)
Bayesian ensemble refinement by replica simulations and reweighting. The Journal of Chemical Physics 118.
Journal Article
5, 17341 (2015)
Assembly of the MHC I peptideloading complex determined by a conserved ionic lock-switch. Scientific Reports 119.
Journal Article
112 (46), pp. 14248 - 14253 (2015)
On artifacts in single-molecule force spectroscopy. Proceedings of the National Academy of Sciences of the United States of America 120.
Journal Article
350 (6259), pp. 445 - 450 (2015)
Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation. Science 121.
Journal Article
63 (1), pp. 85 - 95 (2015)
MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data. Journal of Biomolecular NMR 122.
Journal Article
112 (34), pp. 10720 - 10725 (2015)
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 123.
Journal Article
119 (29), pp. 9029 - 9037 (2015)
Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models. The Journal of Physical Chemistry B 124.
Journal Article
23 (7), pp. 1156 - 1167 (2015)
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure 125.
Journal Article
112 (18), pp. 5685 - 5690 (2015)
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 126.
Journal Article
23 (5), pp. 809 - 818 (2015)
Solution Structure of the Atg1 Complex: Implications for the Architecture of the Phagophore Assembly Site. Structure 127.
Journal Article
115 (5), pp. 2045 - 2222 (2015)
New Perspectives on Proton Pumping in Cellular Respiration. Chemical Reviews 128.
Journal Article
119 (6), pp. 2611 - 2619 (2015)
Linear Energy Relationships in Ground State Proton Transfer and Excited State Proton-Coupled Electron Transfer. The Journal of Physical Chemistry B 129.
Journal Article
11 (1), pp. 276 - 285 (2015)
Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model. Journal of Chemical Theory and Computation 130.
Journal Article
141 (11), pp. 114102 - 114117 (2014)
Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions. The Journal of Chemical Physics 131.
Journal Article
346 (6207), p. 303 - 303 (2014)
Potassium ions line up. Do K+ ions move in single file through potassium channels? Science Magazine 132.
Journal Article
4 (3), pp. 031037 - 031058 (2014)
Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems. Physical Review X 133.
Journal Article
23 (9), pp. 1275 - 1290 (2014)
A maximum entropy approach to the study of residue-specific backbone angle distributions in α-synuclein, an intrinsically disordered protein. Protein Science 134.
Journal Article
111 (19), pp. 6988 - 6993 (2014)
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 135.
Journal Article
6 (4), pp. 258 - 259 (2014)
Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein. Nature Chemistry 136.
Journal Article
136 (8), pp. 3137 - 3144 (2014)
Calcium Inhibition of Ribonuclease H1 Two-Metal Ion Catalysis. Journal of the American Chemical Society 137.
Journal Article
16 (1), pp. 41 - 61 (2014)
Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics. Entropy 138.
Journal Article
184 (3), pp. 427 - 437 (2013)
Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies. Journal of Structural Biology 139.
Journal Article
110 (44), pp. 17874 - 17879 (2013)
Native contacts determine protein folding mechanisms in atomistic simulations. Proceedings of the National Academy of Sciences of the United States of America 140.
Journal Article
117 (42), pp. 13098 - 13106 (2013)
Evolutionary pressure on the topology of protein interface interaction networks. The Journal of Physical Chemistry B 141.
Journal Article
110 (41), pp. 16468 - 16473 (2013)
Phosphate release coupled to rotary motion of F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America 142.
Journal Article
9 (5), e1003065 (2013)
Interface-resolved network of protein-protein interactions. PLoS Computational Biology 143.
Journal Article
87, 052712 (2013)
Atomic-resolution structural information from scattering experiments on macromolecules in solution. Physical Review E 144.
Journal Article
11 (2), e1001492 (2013)
The molecular mechanism of substrate engagement and immunosuppressant inhibition of calcineurin. PLoS Biology 145.
Journal Article
134 (50), pp. 20544 - 20553 (2012)
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 146.
Journal Article
109 (47), pp. 19256 - 19261 (2012)
Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography. Proceedings of the National Academy of Sciences of the United States of America 147.
Journal Article
8 (10), pp. 3759 - 3768 (2012)
Theory and simulation of ion conduction in the pentameric GLIC channel. Journal of Chemical Theory and Computation 148.
Journal Article
8 (10), e1002736 (2012)
Membrane-elasticity model of Coatless vesicle budding induced by ESCRT complexes. PLoS Computational Biology 149.
Journal Article
5, 87 (2012)
Transition path times for DNA and RNA folding from force spectroscopy. Physics 150.
Journal Article
137 (3), 034110 (2012)
Pair diffusion, hydrodynamic interactions, and available volume in dense fluids. The Journal of Chemical Physics 151.
Journal Article
103 (2), pp. 219 - 227 (2012)
Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction. Biophysical Journal 152.
Journal Article
116 (29), pp. 8573 - 8583 (2012)
Characterization of a dynamic string method for the construction of transition pathways in molecular reactions. The Journal of Physical Chemistry B 153.
Journal Article
137 (4), 044709 (2012)
Entropy of single-file water in (6,6) carbon nanotubes. The Journal of Chemical Physics 154.
Journal Article
20 (5), pp. 874 - 886 (2012)
Solution structure of the ESCRT-I and -II supercomplex: implications for membrane budding and scission. Structure 155.
Journal Article
1817 (4), pp. 526 - 536 (2012)
Proton-pumping mechanism of cytochrome c oxidase: a kinetic master-equation approach. Biochimica et Biophysica Acta: BBA 156.
Journal Article
109 (12), pp. 4431 - 4436 (2012)
Stoichiometry of proton translocation by respiratory complex I and its mechanistic implications. Proceedings of the National Academy of Sciences of the United States of America 157.
Journal Article
33 (4), pp. 453 - 465 (2012)
Convergence and error estimation in free energy calculations using the weighted histogram analysis method. Journal of Computational Chemistry 158.
Journal Article
7 (12), pp. 916 - 924 (2011)
Structural basis of p38α regulation by hematopoietic tyrosine phosphatase. Nature Chemical Biology 159.
Journal Article
133 (43), pp. 17138 - 17141 (2011)
Resting and active states of the ERK2:HePTP complex. Journal of the American Chemical Society 160.
Journal Article
133 (47), pp. 19040 - 19043 (2011)
Energetics of direct and water-mediated proton-coupled electron transfer. Journal of the American Chemical Society 161.
Journal Article
13 (38), pp. 16902 - 16911 (2011)
Diffusion models of protein folding. Physical Chemistry Chemical Physics 162.
Journal Article
13 (34), pp. 15403 - 15417 (2011)
Single-file water in nanopores. Physical Chemistry Chemical Physics 163.
Journal Article
13 (29), pp. 13207 - 13215 (2011)
Energetics and dynamics of proton transfer reactions along short water wires. Physical Chemistry Chemical Physics 164.
Journal Article
108 (23), pp. 9437 - 9442 (2011)
Solution structure of the ESCRT-I complex by small-angle X-ray scattering, EPR, and FRET spectroscopy. Proceedings of the National Academy of Sciences of the United States of America 165.
Journal Article
133 (23), pp. 8934 - 8941 (2011)
Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations. Journal of the American Chemical Society 166.
Journal Article
19 (1), pp. 109 - 116 (2011)
SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions. Structure 167.
Journal Article
108 (2), pp. 603 - 608 (2011)
Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks. Proceedings of the National Academy of Sciences of the United States of America 168.
Journal Article
144 (1), pp. 55 - 66 (2011)
Crystal structure and allosteric activation of protein kinase C βII. Cell 169.
Journal Article
114 (49), pp. 16290 - 16297 (2010)
Water in the polar and nonpolar cavities of the protein interleukin-1β. The Journal of Physical Chemistry B 170.
Journal Article
107 (50), pp. 21441 - 21446 (2010)
Free energy profiles from single-molecule pulling experiments. Proceedings of the National Academy of Sciences of the United States of America 171.
Journal Article
107 (46), pp. 19814 - 19819 (2010)
Pore opening and closing of a pentameric ligand-gated ion channel. Proceedings of the National Academy of Sciences of the United States of America 172.
Journal Article
2 (11), pp. 906 - 907 (2010)
Under water's influence. Nature Chemistry 173.
Journal Article
189 (1), pp. 147 - 154 (2010)
Lubrication by molecularly thin water films confined between nanostructured membranes. The European Physical Journal Special Topics 174.
Journal Article
107 (6), pp. 2381 - 2382 (2010)
Catching a protein in the act. Proceedings of the National Academy of Sciences of the United States of America 175.
Journal Article
132 (3), 034102 (2010)
Error and efficiency of simulated tempering simulations. The Journal of Chemical Physics 176.
Journal Article
107 (3), pp. 1088 - 1093 (2010)
Coordinate-dependent diffusion in protein folding. Proceedings of the National Academy of Sciences of the United States of America 177.
Journal Article
146, pp. 341 - 352 (2010)
Interfacial thermodynamics of confined water near molecularly rough surfaces. Faraday Discussions 178.
Journal Article
103 (26), 268102 (2009)
Biological proton pumping in an oscillating electric field. Physical Review Letters 179.
Journal Article
97 (9), pp. 2456 - 2463 (2009)
Gating transition of pentameric ligand-gated ion channels. Biophysical Journal (Annual Meeting Abstracts) 180.
Journal Article
131 (16), 165102 (2009)
Error and efficiency of replica exchange molecular dynamics simulations. The Journal of Chemical Physics 181.
Journal Article
131 (13), 134104 (2009)
Exploration of effective potential landscapes using coarse reverse integration. The Journal of Chemical Physics 182.
Journal Article
1787 (10), pp. 1205 - 1214 (2009)
Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase. Biochimica et Biophysica Acta (BBA) - General Subjects 183.
Journal Article
30 (11), pp. 1634 - 1641 (2009)
Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H. Journal of Computational Chemistry 184.
Journal Article
106 (33), pp. 13707 - 13712 (2009)
Kinetic gating of the proton pump in cytochrome c oxidase. Proceedings of the National Academy of Sciences of the United States of America 185.
Journal Article
113 (26), pp. 9004 - 9015 (2009)
Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. The Journal of Physical Chemistry B 186.
Journal Article
130 (20), 205102 (2009)
Reactive flux and folding pathways in network models of coarse-grained protein dynamics. The Journal of Chemical Physics 187.
Journal Article
131 (17), pp. 6141 - 6148 (2009)
How mitogen-activated protein kinases recognize and phosphorylate their targets: A QM/MM study. Journal of the American Chemical Society 188.
Journal Article
130 (15), 154110 (2009)
A one-dimensional dipole lattice model for water in narrow nanopores. The Journal of Chemical Physics 189.
Journal Article
17 (3), pp. 406 - 416 (2009)
Hybrid structural model of the complete human ESCRT-0 complex. Structure 190.
Journal Article
323 (5914), pp. 593 - 594 (2009)
Unfolding the secrets of calmodulin. Science 191.
Journal Article
5 (5), pp. 1393 - 1399 (2009)
Thermostat artifacts in replica exchange molecular dynamics simulations. Journal of Chemical Theory and Computation 192.
Journal Article
105 (51), pp. 20130 - 20135 (2008)
Static and dynamic correlations in water at hydrophobic interfaces. Proceedings of the National Academy of Sciences of the United States of America 193.
Journal Article
105 (41), pp. 15755 - 15760 (2008)
Theory, analysis, and interpretation of single-molecule force spectroscopy experiments. Proceedings of the National Academy of Sciences of the United States of America 194.
Journal Article
105 (36), pp. 13218 - 13222 (2008)
Macroscopically ordered water in nanopores. Proceedings of the National Academy of Sciences of the United States of America 195.
Journal Article
105 (35), pp. 12855 - 12860 (2008)
Replica exchange simulations of transient encounter complexes in protein-protein association. Proceedings of the National Academy of Sciences of the United States of America 196.
Journal Article
130 (31), pp. 10141 - 10149 (2008)
Atomistic insights into rhodopsin activation from a dynamic model. Journal of the American Chemical Society 197.
Journal Article
1777 (7-8), pp. 890 - 892 (2008)
Prevention of leak in the proton pump of cytochrome c oxidase. Biochimica et Biophysica Acta (BBA) - General Subjects 198.
Journal Article
95 (1), pp. L07 - L09 (2008)
Are current molecular dynamics force fields too helical? Biophysical Journal 199.
Journal Article
112 (19), pp. 5881 - 5882 (2008)
A tribute to Attila Szabo. The Journal of Physical Chemistry B 200.
Journal Article
112 (19), pp. 5968 - 5976 (2008)
Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules. The Journal of Physical Chemistry B