Publications of Gerhard Hummer
All genres
Journal Article (358)
201.
Journal Article
133 (47), pp. 19040 - 19043 (2011)
Energetics of direct and water-mediated proton-coupled electron transfer. Journal of the American Chemical Society 202.
Journal Article
13 (38), pp. 16902 - 16911 (2011)
Diffusion models of protein folding. Physical Chemistry Chemical Physics 203.
Journal Article
13 (34), pp. 15403 - 15417 (2011)
Single-file water in nanopores. Physical Chemistry Chemical Physics 204.
Journal Article
13 (29), pp. 13207 - 13215 (2011)
Energetics and dynamics of proton transfer reactions along short water wires. Physical Chemistry Chemical Physics 205.
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 206.
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 207.
Journal Article
19 (1), pp. 109 - 116 (2011)
SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions. Structure 208.
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 209.
Journal Article
144 (1), pp. 55 - 66 (2011)
Crystal structure and allosteric activation of protein kinase C βII. Cell 210.
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 211.
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 212.
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 213.
Journal Article
2 (11), pp. 906 - 907 (2010)
Under water's influence. Nature Chemistry 214.
Journal Article
189 (1), pp. 147 - 154 (2010)
Lubrication by molecularly thin water films confined between nanostructured membranes. The European Physical Journal Special Topics 215.
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 216.
Journal Article
132 (3), 034102 (2010)
Error and efficiency of simulated tempering simulations. The Journal of Chemical Physics 217.
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 218.
Journal Article
146, pp. 341 - 352 (2010)
Interfacial thermodynamics of confined water near molecularly rough surfaces. Faraday Discussions 219.
Journal Article
103 (26), 268102 (2009)
Biological proton pumping in an oscillating electric field. Physical Review Letters 220.
Journal Article
97 (9), pp. 2456 - 2463 (2009)
Gating transition of pentameric ligand-gated ion channels. Biophysical Journal (Annual Meeting Abstracts) 221.
Journal Article
131 (16), 165102 (2009)
Error and efficiency of replica exchange molecular dynamics simulations. The Journal of Chemical Physics 222.
Journal Article
131 (13), 134104 (2009)
Exploration of effective potential landscapes using coarse reverse integration. The Journal of Chemical Physics 223.
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 224.
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 225.
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 226.
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 227.
Journal Article
130 (20), 205102 (2009)
Reactive flux and folding pathways in network models of coarse-grained protein dynamics. The Journal of Chemical Physics 228.
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 229.
Journal Article
130 (15), 154110 (2009)
A one-dimensional dipole lattice model for water in narrow nanopores. The Journal of Chemical Physics 230.
Journal Article
17 (3), pp. 406 - 416 (2009)
Hybrid structural model of the complete human ESCRT-0 complex. Structure 231.
Journal Article
323 (5914), pp. 593 - 594 (2009)
Unfolding the secrets of calmodulin. Science 232.
Journal Article
5 (5), pp. 1393 - 1399 (2009)
Thermostat artifacts in replica exchange molecular dynamics simulations. Journal of Chemical Theory and Computation 233.
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 234.
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 235.
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 236.
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 237.
Journal Article
130 (31), pp. 10141 - 10149 (2008)
Atomistic insights into rhodopsin activation from a dynamic model. Journal of the American Chemical Society 238.
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 239.
Journal Article
95 (1), pp. L07 - L09 (2008)
Are current molecular dynamics force fields too helical? Biophysical Journal 240.
Journal Article
112 (19), pp. 5881 - 5882 (2008)
A tribute to Attila Szabo. The Journal of Physical Chemistry B 241.
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 242.
Journal Article
112 (19), pp. 6057 - 6069 (2008)
Coarse master equations for peptide folding dynamics. The Journal of Physical Chemistry B 243.
Journal Article
378 (3), pp. 737 - 748 (2008)
Dynamics of cholesterol exchange in the oxysterol binding protein family. Journal of Molecular Biology 244.
Journal Article
105 (17), pp. 6255 - 6259 (2008)
Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase. Proceedings of the National Academy of Sciences of the United States of America 245.
Journal Article
100 (14), p. 145901 (4) (2008)
Layering and position-dependent diffusive dynamics of confined fluids. Physical Review Letters 246.
Journal Article
4 (4), e1000060 (2008)
Binding-induced folding of a natively unstructured transcription factor. PLoS Computational Biology 247.
Journal Article
130 (12), pp. 3706 - 3707 (2008)
Protein folding kinetics under force from molecular simulation. Journal of the American Chemical Society 248.
Journal Article
77 (3 Pt 1), pp. 030902-1 - 030902-4 (2008)
Peptide folding kinetics from replica exchange molecular dynamics. Physical Review E 249.
Journal Article
375 (5), pp. 1416 - 1433 (2008)
Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. Journal of Molecular Biology (London) 250.
Journal Article
373 (2), pp. 439 - 451 (2007)
Substrate-induced conformational changes and dynamics of UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferase-2. Journal of Molecular Biology 251.
Journal Article
69 (1), pp. 43 - 57 (2007)
Protein conformational transitions explored by mixed elastic network models. Proteins: Structure, Function, and Bioinformatics 252.
Journal Article
104 (38), pp. 14883 - 14884 (2007)
Water pulls the strings in hydrophobic polymer collapse. Proceedings of the National Academy of Sciences of the United States of America 253.
Journal Article
1767 (9), pp. 1102 - 1106 (2007)
Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase. Biochimica et Biophysica Acta: BBA 254.
Journal Article
92 (12), pp. 4188 - 4195 (2007)
Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins. Biophysical Journal (Annual Meeting Abstracts) 255.
Journal Article
129 (23), pp. 7369 - 7377 (2007)
Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion. Journal of the American Chemical Society 256.
Journal Article
12 (6), pp. 973 - 986 (2007)
The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting. Developmental Cell 257.
Journal Article
92 (9), pp. 3032 - 3039 (2007)
Structure and dynamics of parallel beta-sheets, hydrophobic core, and loops in Alzheimer's A beta fibrils. Biophysical Journal (Annual Meeting Abstracts) 258.
Journal Article
367 (3), pp. 752 - 763 (2007)
Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography. Journal of Molecular Biology (London) 259.
Journal Article
129 (9), pp. 2414 - 2415 (2007)
Slow conformational dynamics and unfolding of the calmodulin C-terminal domain. Journal of the American Chemical Society 260.
Journal Article
104 (7), pp. 2169 - 2174 (2007)
Kinetic models of redox-coupled proton pumping. Proceedings of the National Academy of Sciences of the United States of America 261.
Journal Article
105 (2-3), pp. 201 - 207 (2007)
Water, proton, and ion transport: from nanotubes to proteins. Molecular Physics 262.
Journal Article
97 (24), 245901 (2006)
Kinetics and mechanism of proton transport across membrane nanopores. Physical Review Letters 263.
Journal Article
97 (2), 020601 (2006)
Identity of distributions of direct uphill and downhill translocation times for particles traversing membrane channels. Physical Review Letters 264.
Journal Article
97 (2), 020601 (2006)
Identity of distributions of direct uphill and downhill translocation times for particles traversing membrane channels. Physical Review Letters 265.
Journal Article
96 (22), 228104 (2006)
Diffusive model of protein folding dynamics with Kramers turnover in rate. Physical Review Letters 266.
Journal Article
124 (20), 204510 (2006)
Effects of electric fields on proton transport through water chains. The Journal of Chemical Physics 267.
Journal Article
96 (10), 108101 (2006)
Intrinsic rates and activation free energies from single-molecule pulling experiments. Physical Review Letters 268.
Journal Article
13 (12), pp. 1755 - 1763 (2005)
Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressor. Structure 269.
Journal Article
102 (46), pp. 16668 - 16671 (2005)
Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation. Proceedings of the National Academy of Sciences of the United States of America 270.
Journal Article
353 (4), pp. 804 - 821 (2005)
Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments. Journal of Molecular Biology (London) 271.
Journal Article
123 (19), 194502 (2005)
Effect of flexibility on hydrophobic behavior of nanotube water channels. The Journal of Chemical Physics 272.
Journal Article
89 (4), pp. 2222 - 2234 (2005)
Ion transport through membrane-spanning nanopores studied by molecular dynamics simulations and continuum electrostatics calculations. Biophysical Journal 273.
Journal Article
89, pp. 2222 - 2234 (2005)
Ion Transport through Membrane-Spanning Nanopores Studiedby Molecular Dynamics Simulations and ContinuumElectrostatics Calculations. Biophysical Journal 274.
Journal Article
95 (13), 130603 (2005)
Coarse nonlinear dynamics and metastability of filling-emptying transitions: water in carbon nanotubes. Physical Review Letters 275.
Journal Article
95 (13), 130603 (2005)
Coarse nonlinear dynamics and metastability of filling-emptying transitions: water in carbon nanotubes. Physical Review Letters 276.
Journal Article
38 (7), pp. 504 - 513 (2005)
Free energy surfaces from single-molecule force spectroscopy. Accounts of Chemical Research 277.
Journal Article
102 (19), pp. 6732 - 6737 (2005)
Reaction coordinates and rates from transition paths. Proceedings of the National Academy of Sciences of the United States of America 278.
Journal Article
48 (8), pp. 3036 - 3044 (2005)
Differential inhibition of HIV-1 and SIV envelope-mediated cell fusion by C34 peptides derived from the C-terminal heptad repeat of gp41 from diverse strains of HIV-1, HIV-2, and SIV. Journal of Medicinal Chemistry 279.
Journal Article
109 (14), pp. 6479 - 6484 (2005)
Coarse master equation from Bayesian analysis of replica molecular dynamics simulations. The Journal of Physical Chemistry B 280.
Journal Article
7, 34 (2005)
Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations. New Journal of Physics 281.
Journal Article
101 (49), pp. 17002 - 17005 (2004)
Water clusters in nonpolar cavities. Proceedings of the National Academy of Sciences of the United States of America 282.
Journal Article
101 (43), pp. 15330 - 15334 (2004)
Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America 283.
Journal Article
121 (16), pp. 7955 - 7965 (2004)
Electric field and temperature effects on water in the narrow nonpolar pores of carbon nanotubes. The Journal of Chemical Physics 284.
Journal Article
108 (40), pp. 15873 - 15879 (2004)
System-Size Dependence of Diffusion Coefficients and Viscosities from Molecular Dynamics Simulations with Periodic Boundary Conditions. The Journal of Physical Chemistry B 285.
Journal Article
101 (33), pp. 12177 - 12182 (2004)
Nucleic acid transport through carbon nanotube membranes. Proceedings of the National Academy of Sciences of the United States of America 286.
Journal Article
50 (7), pp. 1346 - 1355 (2004)
Equation-Free: The Computer-Aided Analysis of Complex Multiscale Systems. AIChE-Journal 287.
Journal Article
86 (6), pp. 3444 - 3460 (2004)
Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phases. Biophysical Journal (Annual Meeting Abstracts) 288.
Journal Article
86 (2), pp. 681 - 689 (2004)
Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations. Biophysical Journal (Annual Meeting Abstracts) 289.
Journal Article
120 (2), pp. 516 - 523 (2004)
From transition paths to transition states and rate coefficients. The Journal of Chemical Physics 290.
Journal Article
108 (2), pp. 544 - 549 (2004)
Methane Partitioning and ransport in Hydrated Carbon Nanotubes. The Journal of Physical Chemistry B 291.
Journal Article
100 (18), pp. 10175 - 10180 (2003)
Osmotic water transport through carbon nanotube membranes. Proceedings of the National Academy of Sciences of the United States of America 292.
Journal Article
85 (1), pp. 5 - 15 (2003)
Kinetics from nonequilibrium single-molecule pulling experiments. Biophysical Journal (Annual Meeting Abstracts) 293.
Journal Article
118 (23), pp. 10762 - 10773 (2003)
Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations. The Journal of Chemical Physics 294.
Journal Article
1604 (2), pp. 61 - 65 (2003)
Water-gated mechanism of proton translocation by cytochrome c oxidase. Biochimica et Biophysica Acta: BBA 295.
Journal Article
665 (1), pp. 267 - 272 (2003)
Random Walk Model for Single‐File Transport of Water Molecules through Carbon Nanotubes. AIP Conference Proceedings 296.
Journal Article
125 (13), pp. 3931 - 3940 (2003)
Protein side-chain motion and hydration in proton-transfer pathways. Results for cytochrome p450cam. Journal of the American Chemical Society 297.
Journal Article
90 (10), 105902 (2003)
Proton transport through water-filled carbon nanotubes. Physical Review Letters 298.
Journal Article
318 (1), pp. 293 - 301 (2003)
Dynamic proton transfer pathways in proteins: role of sidechain conformational fluctuations. Physica A: Statistical and Theoretical Physics 299.
Journal Article
117 (23), pp. 10789 - 10795 (2002)
Filling and emptying kinetics of carbon nanotubes in water. The Journal of Chemical Physics 300.
Journal Article
89 (6), 064503 (2002)
Single-file transport of water molecules through a carbon nanotube. Physical Review Letters