Research Groups

 

Publications of Gerhard Hummer (Results: 154)

 

Intrinsic map dynamics exploration for uncharted effective free-energy landscapes.
Proceedings of the National Academy of Sciences of the United States of America
Chiavazzo E, Covino R, Coifman RR, Gear CW, Georgiou AS, Hummer G, Kevrekidis IG PubMed
Jun 2017 Volume: Issue: Pages:

Helical jackknives control the gates of the double-pore K(+) uptake system KtrAB.
eLife
Diskowski M, Mehdipour AR, Wunnicke D, Mills DJ, Mikusevic V, Bärland N, Hoffmann J, Morgner N, Steinhoff HJ, Hummer G, Vonck J, Hänelt I PubMed
May 2017 Volume: 6 Issue: Pages:

Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis.
eLife
Malinverni D, Jost Lopez A, De Los Rios P, Hummer G, Barducci A PubMed
May 2017 Volume: 6 Issue: Pages:

Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes.
Journal of chemical theory and computation
Ghysels A, Venable RM, Pastor RW, Hummer G PubMed
Jun 2017 Volume: 13 Issue: 6 Pages: 2962-2976

Molecule Counts in Localization Microscopy with Organic Fluorophores.
Chemphyschem : a European journal of chemical physics and physical chemistry
Karathanasis C, Fricke F, Hummer G, Heilemann M PubMed
Apr 2017 Volume: 18 Issue: 8 Pages: 942-948

Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies.
The journal of physical chemistry. A
Simonson T, Hummer G, Roux B PubMed
Feb 2017 Volume: 121 Issue: 7 Pages: 1525-1530

Carbon Nanotubes Mediate Fusion of Lipid Vesicles.
ACS nano
Bhaskara RM, Linker SM, Vögele M, Köfinger J, Hummer G PubMed
Feb 2017 Volume: 11 Issue: 2 Pages: 1273-1280

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
Nöll A, Thomas C, Herbring V, Zollmann T, Barth K, Mehdipour AR, Tomasiak TM, Brüchert S, Joseph B, Abele R, Oliéric V, Wang M, Diederichs K, Hummer G, Stroud RM, Pos KM, Tampé R PubMed
Jan 2017 Volume: 114 Issue: 4 Pages: E438-E447

Systematic evaluation of CS-Rosetta for membrane protein structure prediction with sparse NOE restraints.
Proteins
Reichel K, Fisette O, Braun T, Lange OF, Hummer G, Schäfer LV PubMed
May 2017 Volume: 85 Issue: 5 Pages: 812-826

Model-independent counting of molecules in single-molecule localization microscopy.
Molecular biology of the cell
Hummer G, Fricke F, Heilemann M PubMed
Nov 2016 Volume: 27 Issue: 22 Pages: 3637-3644

Dynamics of the Orientational Factor in Fluorescence Resonance Energy Transfer.
The journal of physical chemistry. B
Hummer G, Szabo A PubMed
Apr 2017 Volume: 121 Issue: 15 Pages: 3331-3339

Antigenic Peptide Recognition on the Human ABC Transporter TAP Resolved by DNP-Enhanced Solid-State NMR Spectroscopy.
Journal of the American Chemical Society
Lehnert E, Mao J, Mehdipour AR, Hummer G, Abele R, Glaubitz C, Tampé R PubMed
Oct 2016 Volume: Issue: Pages:

Kinetic Ductility and Force-Spike Resistance of Proteins from Single-Molecule Force Spectroscopy.
Biophysical journal
Cossio P, Hummer G, Szabo A PubMed
Aug 2016 Volume: 111 Issue: 4 Pages: 832-40

Cardiolipin puts the seal on ATP synthase.
Proceedings of the National Academy of Sciences of the United States of America
Mehdipour AR, Hummer G PubMed
Aug 2016 Volume: 113 Issue: 31 Pages: 8568-70

Divergent Diffusion Coefficients in Simulations of Fluids and Lipid Membranes.
The journal of physical chemistry. B
Vögele M, Hummer G PubMed
Aug 2016 Volume: 120 Issue: 33 Pages: 8722-32

Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers.
The journal of physical chemistry letters
Leahy CT, Murphy RD, Hummer G, Rosta E, Buchete NV PubMed
Jul 2016 Volume: 7 Issue: 14 Pages: 2676-82

A Eukaryotic Sensor for Membrane Lipid Saturation.
Molecular cell
Covino R, Ballweg S, Stordeur C, Michaelis JB, Puth K, Wernig F, Bahrami A, Ernst AM, Hummer G, Ernst R PubMed
Jul 2016 Volume: 63 Issue: 1 Pages: 49-59

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
Sugawa M, Okazaki K, Kobayashi M, Matsui T, Hummer G, Masaike T, Nishizaka T PubMed
May 2016 Volume: 113 Issue: 21 Pages: E2916-24

Microscopic interpretation of folding ϕ-values using the transition path ensemble.
Proceedings of the National Academy of Sciences of the United States of America
Best RB, Hummer G PubMed
Mar 2016 Volume: 113 Issue: 12 Pages: 3263-8

Molecular simulation and modeling of complex I.
Biochimica et biophysica acta
Hummer G, Wikström M PubMed
Jul 2016 Volume: 1857 Issue: 7 Pages: 915-21

Bayesian ensemble refinement by replica simulations and reweighting.
The Journal of chemical physics
Hummer G, Köfinger J PubMed
Dec 2015 Volume: 143 Issue: 24 Pages: 243150

Assembly of the MHC I peptide-loading complex determined by a conserved ionic lock-switch.
Scientific reports
Blees A, Reichel K, Trowitzsch S, Fisette O, Bock C, Abele R, Hummer G, Schäfer LV, Tampé R PubMed
Nov 2015 Volume: 5 Issue: Pages: 17341

Free energies from dynamic weighted histogram analysis using unbiased Markov state model.
Journal of chemical theory and computation
Rosta E, Hummer G PubMed
Jan 2015 Volume: 11 Issue: 1 Pages: 276-85

On artifacts in single-molecule force spectroscopy.
Proceedings of the National Academy of Sciences of the United States of America
Cossio P, Hummer G, Szabo A PubMed
Nov 2015 Volume: 112 Issue: 46 Pages: 14248-53

Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation.
Science (New York, N.Y.)
Barends TR, Foucar L, Ardevol A, Nass K, Aquila A, Botha S, Doak RB, Falahati K, Hartmann E, Hilpert M, Heinz M, Hoffmann MC, Köfinger J, Koglin JE, Kovacsova G, Liang M, Milathianaki D, Lemke HT, Reinstein J, Roome CM, Shoeman RL, Williams GJ, Burghardt I, Hummer G, Boutet S, Schlichting I PubMed
Oct 2015 Volume: 350 Issue: 6259 Pages: 445-50

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
Sharma V, Belevich G, Gamiz-Hernandez AP, Róg T, Vattulainen I, Verkhovskaya ML, Wikström M, Hummer G, Kaila VR PubMed
Sep 2015 Volume: 112 Issue: 37 Pages: 11571-6

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
Okazaki K, Hummer G PubMed
Aug 2015 Volume: 112 Issue: 34 Pages: 10720-5

MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data.
Journal of biomolecular NMR
Mantsyzov AB, Shen Y, Lee JH, Hummer G, Bax A PubMed
Sep 2015 Volume: 63 Issue: 1 Pages: 85-95

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.
Structure (London, England : 1993)
Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD PubMed
Jul 2015 Volume: 23 Issue: 7 Pages: 1156-67

Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems.
Physical review. X
Johnson ME, Hummer G PubMed
Volume: 4 Issue: 3 Pages:

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
Kmita K, Wirth C, Warnau J, Guerrero-Castillo S, Hunte C, Hummer G, Kaila VR, Zwicker K, Brandt U, Zickermann V PubMed
May 2015 Volume: 112 Issue: 18 Pages: 5685-90

Solution structure of the Atg1 complex: implications for the architecture of the phagophore assembly site.
Structure (London, England : 1993)
Köfinger J, Ragusa MJ, Lee IH, Hummer G, Hurley JH PubMed
May 2015 Volume: 23 Issue: 5 Pages: 809-18

New perspectives on proton pumping in cellular respiration.
Chemical reviews
Wikström M, Sharma V, Kaila VR, Hosler JP, Hummer G PubMed
Mar 2015 Volume: 115 Issue: 5 Pages: 2196-221

Preface: special topic on biological water.
The Journal of chemical physics
Hummer G, Tokmakoff A PubMed
Dec 2014 Volume: 141 Issue: 22 Pages: 22D101

Linear energy relationships in ground state proton transfer and excited state proton-coupled electron transfer.
The journal of physical chemistry. B
Gamiz-Hernandez AP, Magomedov A, Hummer G, Kaila VR PubMed
Feb 2015 Volume: 119 Issue: 6 Pages: 2611-9

Biochemistry. Potassium ions line up.
Science (New York, N.Y.)
Hummer G PubMed
Oct 2014 Volume: 346 Issue: 6207 Pages: 303

Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models.
The journal of physical chemistry. B
Hummer G, Szabo A PubMed
Jul 2015 Volume: 119 Issue: 29 Pages: 9029-37

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions.
The Journal of chemical physics
Nedialkova LV, Amat MA, Kevrekidis IG, Hummer G PubMed
Sep 2014 Volume: 141 Issue: 11 Pages: 114102

A maximum entropy approach to the study of residue-specific backbone angle distributions in α-synuclein, an intrinsically disordered protein.
Protein science : a publication of the Protein Society
Mantsyzov AB, Maltsev AS, Ying J, Shen Y, Hummer G, Bax A PubMed
Sep 2014 Volume: 23 Issue: 9 Pages: 1275-90

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
Kaila VR, Wikström M, Hummer G PubMed
May 2014 Volume: 111 Issue: 19 Pages: 6988-93

Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein.
Nature chemistry
Kaila VR, Schotte F, Cho HS, Hummer G, Anfinrud PA PubMed
Apr 2014 Volume: 6 Issue: 4 Pages: 258-9

Calcium inhibition of ribonuclease H1 two-metal ion catalysis.
Journal of the American Chemical Society
Rosta E, Yang W, Hummer G PubMed
Feb 2014 Volume: 136 Issue: 8 Pages: 3137-44

Nobel 2013 Chemistry: Methods for computational chemistry.
Nature
Thiel W, Hummer G PubMed
Dec 2013 Volume: 504 Issue: 7478 Pages: 96-7

Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies.
Journal of structural biology
Cossio P, Hummer G PubMed
Dec 2013 Volume: 184 Issue: 3 Pages: 427-37

Native contacts determine protein folding mechanisms in atomistic simulations.
Proceedings of the National Academy of Sciences of the United States of America
Best RB, Hummer G, Eaton WA PubMed
Oct 2013 Volume: 110 Issue: 44 Pages: 17874-9

Phosphate release coupled to rotary motion of F1-ATPase.
Proceedings of the National Academy of Sciences of the United States of America
Okazaki K, Hummer G PubMed
Oct 2013 Volume: 110 Issue: 41 Pages: 16468-73

Atomic-resolution structural information from scattering experiments on macromolecules in solution.
Physical review. E, Statistical, nonlinear, and soft matter physics
Köfinger J, Hummer G PubMed
May 2013 Volume: 87 Issue: 5 Pages: 052712

Evolutionary pressure on the topology of protein interface interaction networks.
The journal of physical chemistry. B
Johnson ME, Hummer G PubMed
Oct 2013 Volume: 117 Issue: 42 Pages: 13098-106

Interface-resolved network of protein-protein interactions.
PLoS computational biology
Johnson ME, Hummer G PubMed
2013 Volume: 9 Issue: 5 Pages: e1003065

The molecular mechanism of substrate engagement and immunosuppressant inhibition of calcineurin.
PLoS biology
Grigoriu S, Bond R, Cossio P, Chen JA, Ly N, Hummer G, Page R, Cyert MS, Peti W PubMed
2013 Volume: 11 Issue: 2 Pages: e1001492

Theory and simulation of ion conduction in the pentameric GLIC channel.
Journal of chemical theory and computation
Zhu F, Hummer G PubMed
Oct 2012 Volume: 8 Issue: 10 Pages: 3759-3768

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
Lans I, Medina M, Rosta E, Hummer G, Garcia-Viloca M, Lluch JM, González-Lafont À PubMed
Dec 2012 Volume: 134 Issue: 50 Pages: 20544-53

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
Schotte F, Cho HS, Kaila VR, Kamikubo H, Dashdorj N, Henry ER, Graber TJ, Henning R, Wulff M, Hummer G, Kataoka M, Anfinrud PA PubMed
Nov 2012 Volume: 109 Issue: 47 Pages: 19256-61

Membrane-elasticity model of Coatless vesicle budding induced by ESCRT complexes.
PLoS computational biology
Różycki B, Boura E, Hurley JH, Hummer G PubMed
2012 Volume: 8 Issue: 10 Pages: e1002736

Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction.
Biophysical journal
Zhu F, Hummer G PubMed
Jul 2012 Volume: 103 Issue: 2 Pages: 219-27

Entropy of single-file water in (6,6) carbon nanotubes.
The Journal of chemical physics
Waghe A, Rasaiah JC, Hummer G PubMed
Jul 2012 Volume: 137 Issue: 4 Pages: 044709

Pair diffusion, hydrodynamic interactions, and available volume in dense fluids.
The Journal of chemical physics
Mittal J, Hummer G PubMed
Jul 2012 Volume: 137 Issue: 3 Pages: 034110

Characterization of a dynamic string method for the construction of transition pathways in molecular reactions.
The journal of physical chemistry. B
Johnson ME, Hummer G PubMed
Jul 2012 Volume: 116 Issue: 29 Pages: 8573-83

Solution structure of the ESCRT-I and -II supercomplex: implications for membrane budding and scission.
Structure (London, England : 1993)
Boura E, Różycki B, Chung HS, Herrick DZ, Canagarajah B, Cafiso DS, Eaton WA, Hummer G, Hurley JH PubMed
May 2012 Volume: 20 Issue: 5 Pages: 874-86

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
Wikström M, Hummer G PubMed
Mar 2012 Volume: 109 Issue: 12 Pages: 4431-6

Convergence and error estimation in free energy calculations using the weighted histogram analysis method.
Journal of computational chemistry
Zhu F, Hummer G PubMed
Feb 2012 Volume: 33 Issue: 4 Pages: 453-65

Structural basis of p38α regulation by hematopoietic tyrosine phosphatase.
Nature chemical biology
Francis DM, Różycki B, Koveal D, Hummer G, Page R, Peti W PubMed
Nov 2011 Volume: 7 Issue: 12 Pages: 916-24

Energetics of direct and water-mediated proton-coupled electron transfer.
Journal of the American Chemical Society
Kaila VR, Hummer G PubMed
Nov 2011 Volume: 133 Issue: 47 Pages: 19040-3

Resting and active states of the ERK2:HePTP complex.
Journal of the American Chemical Society
Francis DM, Różycki B, Tortajada A, Hummer G, Peti W, Page R PubMed
Nov 2011 Volume: 133 Issue: 43 Pages: 17138-41

Proton-pumping mechanism of cytochrome c oxidase: a kinetic master-equation approach.
Biochimica et biophysica acta
Kim YC, Hummer G PubMed
Apr 2012 Volume: 1817 Issue: 4 Pages: 526-36

Diffusion models of protein folding.
Physical chemistry chemical physics : PCCP
Best RB, Hummer G PubMed
Oct 2011 Volume: 13 Issue: 38 Pages: 16902-11

Single-file water in nanopores.
Physical chemistry chemical physics : PCCP
Köfinger J, Hummer G, Dellago C PubMed
Sep 2011 Volume: 13 Issue: 34 Pages: 15403-17

Energetics and dynamics of proton transfer reactions along short water wires.
Physical chemistry chemical physics : PCCP
Kaila VR, Hummer G PubMed
Aug 2011 Volume: 13 Issue: 29 Pages: 13207-15

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
Boura E, Rózycki B, Herrick DZ, Chung HS, Vecer J, Eaton WA, Cafiso DS, Hummer G, Hurley JH PubMed
Jun 2011 Volume: 108 Issue: 23 Pages: 9437-42

Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations.
Journal of the American Chemical Society
Rosta E, Nowotny M, Yang W, Hummer G PubMed
Jun 2011 Volume: 133 Issue: 23 Pages: 8934-41

SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions.
Structure (London, England : 1993)
Różycki B, Kim YC, Hummer G PubMed
Jan 2011 Volume: 19 Issue: 1 Pages: 109-16

Crystal structure and allosteric activation of protein kinase C βII.
Cell
Leonard TA, Różycki B, Saidi LF, Hummer G, Hurley JH PubMed
Jan 2011 Volume: 144 Issue: 1 Pages: 55-66

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
Johnson ME, Hummer G PubMed
Jan 2011 Volume: 108 Issue: 2 Pages: 603-8

Free energy profiles from single-molecule pulling experiments.
Proceedings of the National Academy of Sciences of the United States of America
Hummer G, Szabo A PubMed
Dec 2010 Volume: 107 Issue: 50 Pages: 21441-6

Water in the polar and nonpolar cavities of the protein interleukin-1β.
The journal of physical chemistry. B
Yin H, Feng G, Clore GM, Hummer G, Rasaiah JC PubMed
Dec 2010 Volume: 114 Issue: 49 Pages: 16290-7

Interfacial thermodynamics of confined water near molecularly rough surfaces.
Faraday discussions
Mittal J, Hummer G PubMed
2010 Volume: 146 Issue: Pages: 341-52; discussion 367-93, 395-401

Pore opening and closing of a pentameric ligand-gated ion channel.
Proceedings of the National Academy of Sciences of the United States of America
Zhu F, Hummer G PubMed
Nov 2010 Volume: 107 Issue: 46 Pages: 19814-9

Molecular binding: Under water's influence.
Nature chemistry
Hummer G PubMed
Nov 2010 Volume: 2 Issue: 11 Pages: 906-7

Biological proton pumping in an oscillating electric field.
Physical review letters
Kim YC, Furchtgott LA, Hummer G PubMed
Dec 2009 Volume: 103 Issue: 26 Pages: 268102

Catching a protein in the act.
Proceedings of the National Academy of Sciences of the United States of America
Hummer G PubMed
Feb 2010 Volume: 107 Issue: 6 Pages: 2381-2

Error and efficiency of simulated tempering simulations.
The Journal of chemical physics
Rosta E, Hummer G PubMed
Jan 2010 Volume: 132 Issue: 3 Pages: 034102

Coordinate-dependent diffusion in protein folding.
Proceedings of the National Academy of Sciences of the United States of America
Best RB, Hummer G PubMed
Jan 2010 Volume: 107 Issue: 3 Pages: 1088-93

Thermostat artifacts in replica exchange molecular dynamics simulations.
Journal of chemical theory and computation
Rosta E, Buchete NV, Hummer G PubMed
2009 Volume: 5 Issue: 5 Pages: 1393-1399

Error and efficiency of replica exchange molecular dynamics simulations.
The Journal of chemical physics
Rosta E, Hummer G PubMed
Oct 2009 Volume: 131 Issue: 16 Pages: 165102

Gating transition of pentameric ligand-gated ion channels.
Biophysical journal
Zhu F, Hummer G PubMed
Nov 2009 Volume: 97 Issue: 9 Pages: 2456-63

Exploration of effective potential landscapes using coarse reverse integration.
The Journal of chemical physics
Frewen TA, Hummer G, Kevrekidis IG PubMed
Oct 2009 Volume: 131 Issue: 13 Pages: 134104

Kinetic gating of the proton pump in cytochrome c oxidase.
Proceedings of the National Academy of Sciences of the United States of America
Kim YC, Wikström M, Hummer G PubMed
Aug 2009 Volume: 106 Issue: 33 Pages: 13707-12

Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.
The journal of physical chemistry. B
Best RB, Hummer G PubMed
Jul 2009 Volume: 113 Issue: 26 Pages: 9004-15

Reactive flux and folding pathways in network models of coarse-grained protein dynamics.
The Journal of chemical physics
Berezhkovskii A, Hummer G, Szabo A PubMed
May 2009 Volume: 130 Issue: 20 Pages: 205102

Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H.
Journal of computational chemistry
Rosta E, Woodcock HL, Brooks BR, Hummer G PubMed
Aug 2009 Volume: 30 Issue: 11 Pages: 1634-41

Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase.
Biochimica et biophysica acta
Kaila VR, Verkhovsky MI, Hummer G, Wikström M PubMed
Oct 2009 Volume: 1787 Issue: 10 Pages: 1205-14

A one-dimensional dipole lattice model for water in narrow nanopores.
The Journal of chemical physics
Köfinger J, Hummer G, Dellago C PubMed
Apr 2009 Volume: 130 Issue: 15 Pages: 154110

How mitogen-activated protein kinases recognize and phosphorylate their targets: A QM/MM study.
Journal of the American Chemical Society
Turjanski AG, Hummer G, Gutkind JS PubMed
May 2009 Volume: 131 Issue: 17 Pages: 6141-8

Hybrid structural model of the complete human ESCRT-0 complex.
Structure (London, England : 1993)
Ren X, Kloer DP, Kim YC, Ghirlando R, Saidi LF, Hummer G, Hurley JH PubMed
Mar 2009 Volume: 17 Issue: 3 Pages: 406-16

Biochemistry. Unfolding the secrets of calmodulin.
Science (New York, N.Y.)
Best RB, Hummer G PubMed
Jan 2009 Volume: 323 Issue: 5914 Pages: 593-4

Static and dynamic correlations in water at hydrophobic interfaces.
Proceedings of the National Academy of Sciences of the United States of America
Mittal J, Hummer G PubMed
Dec 2008 Volume: 105 Issue: 51 Pages: 20130-5

Theory, analysis, and interpretation of single-molecule force spectroscopy experiments.
Proceedings of the National Academy of Sciences of the United States of America
Dudko OK, Hummer G, Szabo A PubMed
Oct 2008 Volume: 105 Issue: 41 Pages: 15755-60

Macroscopically ordered water in nanopores.
Proceedings of the National Academy of Sciences of the United States of America
Köfinger J, Hummer G, Dellago C PubMed
Sep 2008 Volume: 105 Issue: 36 Pages: 13218-22

Replica exchange simulations of transient encounter complexes in protein-protein association.
Proceedings of the National Academy of Sciences of the United States of America
Kim YC, Tang C, Clore GM, Hummer G PubMed
Sep 2008 Volume: 105 Issue: 35 Pages: 12855-60

Atomistic insights into rhodopsin activation from a dynamic model.
Journal of the American Chemical Society
Tikhonova IG, Best RB, Engel S, Gershengorn MC, Hummer G, Costanzi S PubMed
Aug 2008 Volume: 130 Issue: 31 Pages: 10141-9

Layering and position-dependent diffusive dynamics of confined fluids.
Physical review letters
Mittal J, Truskett TM, Errington JR, Hummer G PubMed
Apr 2008 Volume: 100 Issue: 14 Pages: 145901

Peptide folding kinetics from replica exchange molecular dynamics.
Physical review. E, Statistical, nonlinear, and soft matter physics
Buchete NV, Hummer G PubMed
Mar 2008 Volume: 77 Issue: 3 Pt 1 Pages: 030902

A tribute to Attila Szabo.
The journal of physical chemistry. B
Eaton WA, Hummer G, Zwanzig RW PubMed
May 2008 Volume: 112 Issue: 19 Pages: 5881-91

Are current molecular dynamics force fields too helical?
Biophysical journal
Best RB, Buchete NV, Hummer G PubMed
Jul 2008 Volume: 95 Issue: 1 Pages: L07-9

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
Kaila VR, Verkhovsky MI, Hummer G, Wikström M PubMed
Apr 2008 Volume: 105 Issue: 17 Pages: 6255-9

Prevention of leak in the proton pump of cytochrome c oxidase.
Biochimica et biophysica acta
Kaila VR, Verkhovsky M, Hummer G, Wikström M PubMed
Volume: 1777 Issue: 7-8 Pages: 890-2

Binding-induced folding of a natively unstructured transcription factor.
PLoS computational biology
Turjanski AG, Gutkind JS, Best RB, Hummer G PubMed
Apr 2008 Volume: 4 Issue: 4 Pages: e1000060

Dynamics of cholesterol exchange in the oxysterol binding protein family.
Journal of molecular biology
Canagarajah BJ, Hummer G, Prinz WA, Hurley JH PubMed
May 2008 Volume: 378 Issue: 3 Pages: 737-48

Protein folding kinetics under force from molecular simulation.
Journal of the American Chemical Society
Best RB, Hummer G PubMed
Mar 2008 Volume: 130 Issue: 12 Pages: 3706-7

Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules.
The journal of physical chemistry. B
Best RB, Paci E, Hummer G, Dudko OK PubMed
May 2008 Volume: 112 Issue: 19 Pages: 5968-76

Coarse master equations for peptide folding dynamics.
The journal of physical chemistry. B
Buchete NV, Hummer G PubMed
May 2008 Volume: 112 Issue: 19 Pages: 6057-69

Water in nonpolar confinement: from nanotubes to proteins and beyond.
Annual review of physical chemistry
Rasaiah JC, Garde S, Hummer G PubMed
2008 Volume: 59 Issue: Pages: 713-40

Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding.
Journal of molecular biology
Kim YC, Hummer G PubMed
Feb 2008 Volume: 375 Issue: 5 Pages: 1416-33

Water pulls the strings in hydrophobic polymer collapse.
Proceedings of the National Academy of Sciences of the United States of America
Hummer G PubMed
Sep 2007 Volume: 104 Issue: 38 Pages: 14883-4

Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase.
Biochimica et biophysica acta
Tuukkanen A, Kaila VR, Laakkonen L, Hummer G, Wikström M PubMed
Sep 2007 Volume: 1767 Issue: 9 Pages: 1102-6

Protein conformational transitions explored by mixed elastic network models.
Proteins
Zheng W, Brooks BR, Hummer G PubMed
Oct 2007 Volume: 69 Issue: 1 Pages: 43-57

The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting.
Developmental cell
Prag G, Watson H, Kim YC, Beach BM, Ghirlando R, Hummer G, Bonifacino JS, Hurley JH PubMed
Jun 2007 Volume: 12 Issue: 6 Pages: 973-86

Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion.
Journal of the American Chemical Society
Yin H, Hummer G, Rasaiah JC PubMed
Jun 2007 Volume: 129 Issue: 23 Pages: 7369-77

Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins.
Biophysical journal
Dudko OK, Mathé J, Szabo A, Meller A, Hummer G PubMed
Jun 2007 Volume: 92 Issue: 12 Pages: 4188-95

Structure and dynamics of parallel beta-sheets, hydrophobic core, and loops in Alzheimer's A beta fibrils.
Biophysical journal
Buchete NV, Hummer G PubMed
May 2007 Volume: 92 Issue: 9 Pages: 3032-9

Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography.
Journal of molecular biology
Collins MD, Quillin ML, Hummer G, Matthews BW, Gruner SM PubMed
Mar 2007 Volume: 367 Issue: 3 Pages: 752-63

Slow conformational dynamics and unfolding of the calmodulin C-terminal domain.
Journal of the American Chemical Society
Chen YG, Hummer G PubMed
Mar 2007 Volume: 129 Issue: 9 Pages: 2414-5

Kinetic models of redox-coupled proton pumping.
Proceedings of the National Academy of Sciences of the United States of America
Kim YC, Wikström M, Hummer G PubMed
Feb 2007 Volume: 104 Issue: 7 Pages: 2169-74

Kinetics and mechanism of proton transport across membrane nanopores.
Physical review letters
Dellago C, Hummer G PubMed
Dec 2006 Volume: 97 Issue: 24 Pages: 245901

Identity of distributions of direct uphill and downhill translocation times for particles traversing membrane channels.
Physical review letters
Berezhkovskii AM, Hummer G, Bezrukov SM PubMed
Jul 2006 Volume: 97 Issue: 2 Pages: 020601

Coarse master equation from Bayesian analysis of replica molecular dynamics simulations.
The journal of physical chemistry. B
Sriraman S, Kevrekidis IG, Hummer G PubMed
Apr 2005 Volume: 109 Issue: 14 Pages: 6479-84

Diffusive model of protein folding dynamics with Kramers turnover in rate.
Physical review letters
Best RB, Hummer G PubMed
Jun 2006 Volume: 96 Issue: 22 Pages: 228104

Effects of electric fields on proton transport through water chains.
The Journal of chemical physics
Hassan SA, Hummer G, Lee YS PubMed
May 2006 Volume: 124 Issue: 20 Pages: 204510

Intrinsic rates and activation free energies from single-molecule pulling experiments.
Physical review letters
Dudko OK, Hummer G, Szabo A PubMed
Mar 2006 Volume: 96 Issue: 10 Pages: 108101

Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressor.
Structure (London, England : 1993)
Best RB, Chen YG, Hummer G PubMed
Dec 2005 Volume: 13 Issue: 12 Pages: 1755-63

Effect of flexibility on hydrophobic behavior of nanotube water channels.
The Journal of chemical physics
Andreev S, Reichman D, Hummer G PubMed
Nov 2005 Volume: 123 Issue: 19 Pages: 194502

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
Collins MD, Hummer G, Quillin ML, Matthews BW, Gruner SM PubMed
Nov 2005 Volume: 102 Issue: 46 Pages: 16668-71

Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments.
Journal of molecular biology
Buchete NV, Tycko R, Hummer G PubMed
Nov 2005 Volume: 353 Issue: 4 Pages: 804-21

Coarse nonlinear dynamics and metastability of filling-emptying transitions: water in carbon nanotubes.
Physical review letters
Sriraman S, Kevrekidis IG, Hummer G PubMed
Sep 2005 Volume: 95 Issue: 13 Pages: 130603

Free energy surfaces from single-molecule force spectroscopy.
Accounts of chemical research
Hummer G, Szabo A PubMed
Jul 2005 Volume: 38 Issue: 7 Pages: 504-13

Ion transport through membrane-spanning nanopores studied by molecular dynamics simulations and continuum electrostatics calculations.
Biophysical journal
Peter C, Hummer G PubMed
Oct 2005 Volume: 89 Issue: 4 Pages: 2222-34

Comment on "Force-clamp spectroscopy monitors the folding trajectory of a single protein".
Science (New York, N.Y.)
Best RB, Hummer G PubMed
Apr 2005 Volume: 308 Issue: 5721 Pages: 498; author reply 498

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
Gustchina E, Hummer G, Bewley CA, Clore GM PubMed
Apr 2005 Volume: 48 Issue: 8 Pages: 3036-44

Reaction coordinates and rates from transition paths.
Proceedings of the National Academy of Sciences of the United States of America
Best RB, Hummer G PubMed
May 2005 Volume: 102 Issue: 19 Pages: 6732-7

Water clusters in nonpolar cavities.
Proceedings of the National Academy of Sciences of the United States of America
Vaitheeswaran S, Yin H, Rasaiah JC, Hummer G PubMed
Dec 2004 Volume: 101 Issue: 49 Pages: 17002-5

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
Hummer G, Schotte F, Anfinrud PA PubMed
Oct 2004 Volume: 101 Issue: 43 Pages: 15330-4

Electric field and temperature effects on water in the narrow nonpolar pores of carbon nanotubes.
The Journal of chemical physics
Vaitheeswaran S, Rasaiah JC, Hummer G PubMed
Oct 2004 Volume: 121 Issue: 16 Pages: 7955-65

Nucleic acid transport through carbon nanotube membranes.
Proceedings of the National Academy of Sciences of the United States of America
Yeh IC, Hummer G PubMed
Aug 2004 Volume: 101 Issue: 33 Pages: 12177-82

From transition paths to transition states and rate coefficients.
The Journal of chemical physics
Hummer G PubMed
Jan 2004 Volume: 120 Issue: 2 Pages: 516-23

Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phases.
Biophysical journal
Zweckstetter M, Hummer G, Bax A PubMed
Jun 2004 Volume: 86 Issue: 6 Pages: 3444-60

Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations.
Biophysical journal
Yeh IC, Hummer G PubMed
Feb 2004 Volume: 86 Issue: 2 Pages: 681-9

Osmotic water transport through carbon nanotube membranes.
Proceedings of the National Academy of Sciences of the United States of America
Kalra A, Garde S, Hummer G PubMed
Sep 2003 Volume: 100 Issue: 18 Pages: 10175-80

Kinetics from nonequilibrium single-molecule pulling experiments.
Biophysical journal
Hummer G, Szabo A PubMed
Jul 2003 Volume: 85 Issue: 1 Pages: 5-15

Water-gated mechanism of proton translocation by cytochrome c oxidase.
Biochimica et biophysica acta
Wikström M, Verkhovsky MI, Hummer G PubMed
Jun 2003 Volume: 1604 Issue: 2 Pages: 61-5

Proton transport through water-filled carbon nanotubes.
Physical review letters
Dellago C, Naor MM, Hummer G PubMed
Mar 2003 Volume: 90 Issue: 10 Pages: 105902

Protein side-chain motion and hydration in proton-transfer pathways. Results for cytochrome p450cam.
Journal of the American Chemical Society
Taraphder S, Hummer G PubMed
Apr 2003 Volume: 125 Issue: 13 Pages: 3931-40

Single-file transport of water molecules through a carbon nanotube.
Physical review letters
Berezhkovskii A, Hummer G PubMed
Aug 2002 Volume: 89 Issue: 6 Pages: 064503

Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent.
Journal of the American Chemical Society
Yeh IC, Hummer G PubMed
Jun 2002 Volume: 124 Issue: 23 Pages: 6563-8

Hydrophobicity maps of the N-peptide coiled coil of HIV-1 gp41.
Biochemistry
Siebert X, Hummer G PubMed
Mar 2002 Volume: 41 Issue: 9 Pages: 2956-61