Zhu F, Hummer G, Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction. Biophys J (103):219-27, 2012. [PMID: 22853899]
Johnson ME, Hummer G, Characterization of a dynamic string method for the construction of transition pathways in molecular reactions. J Phys Chem B (116):8573-83, 2012. [PMID: 22616575]
Hummer G, Eaton WA, Viewpoint: Transition path times for DNA and RNA folding from force spectroscopy. Physics (5):87, 2012. [Full text/Abstract]
Mittal J, Hummer G, Pair diffusion, hydrodynamic interactions, and available volume in dense fluids. J Chem Phys (137):034110, 2012. [PMID: 22830686]
Waghe A, Rasaiah JC, Hummer G, Entropy of single-file water in (6, 6) carbon nanotubes. J Chem Phys (137):044709, 2012. [PMID: 22852646]
Wikström M, Hummer G, Stoichiometry of proton translocation by respiratory Complex I and its mechanistic implications. Proc Natl Acad Sci USA (109):4431-6, 2012. [PMID: 22392981]
Boura E, Rozycki B, Chung HS, Herrick DZ, Canagarajah B, Cafiso D, Eaton WA, Hummer G, Hurley JH, Solution structure of the ESCRT-I and -II supercomplex: implications for membrane budding and scission. Structure (20):874-86, 2012. [PMID: 22579254]
Kim YC, Hummer G, Proton-pumping mechanism of cytochrome c oxidase: A kinetic master-equation approach. Biochim Biophys Acta-Bioenergetics (1817):526-36, 2012. [PMID: 21946020]
Zhu F, Hummer G, Convergence and error estimation in free energy calculations using the weighted histogram analysis method. J Comp Chem (33):453-65, 2012. [PMID: 22109354]
Francis DM, Rozycki B, Koveal D, Hummer G, Page R, Peti W, Structural basis of p38α regulation and specificity by hematopoietic tyrosine phosphatase. Nature Chem Biol (7):916-24, 2011. [PMID: 22057126]
Francis DM, Rozycki B, Tortajada A, Hummer G, Peti W, Page R, Resting and Active States of the ERK2:HePTP Complex. J Am Chem Soc (133):17138–41, 2011. [PMID: 21985012] [Full text/Abstract]
Kaila VRI, Hummer G, Energetics of direct and water-mediated proton-coupled electron transfer. J Am Chem Soc (133):19040–3, 2011. [PMID: 21988482]
Best RB, Hummer G, Diffusion models of protein folding. Phys Chem Chem Phys (13):1690-11, 2011. [PMID: 21842082]
Köfinger J, Hummer G, Dellago C, Single-file water in nanopores. Phys Chem Chem Phys (13):15403-17, 2011. [PMID: 21779552]
Kaila VRI, Hummer G, Energetics and dynamics of proton transfer reactions along short water wires. Phys Chem Chem Phys 13, 13207-15, 2011. [PMID: 21701719]
Rosta E, Nowotny M, Yang W, Hummer G, Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations. J Am Chem Soc 133, 8934-41, 2011. [PMID: 21539371]
Boura E, Rozycki B, Herrick DZ, Chung HS, Vecer J, Eaton WA, Cafiso D, Hummer G, Hurley JH, Solution structure of the ESCRT-I complex by small angle x-ray scattering, EPR, and FRET spectroscopy. Proc Natl Acad Sci USA 108, 9437-42, 2011. [PMID: 21596998] [Full text/Abstract]
Johnson ME, Hummer G Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks. Proc Natl Acad Sci USA(108):603-8, 2011. [PMID: 21187424] [Full text/Abstract]
Rozycki B, Kim YC, Hummer G SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions. Structure (19):109-16, 2011. [PMID: 21220121] [Full text/Abstract]
Leonard TA, Rozycki B, Saidi LF, Hummer G, Hurley JH Crystal structure and allosteric activation of protein kinase C bII. Cell (144):55-66, 2011. [PMID: 21215369] [Full text/Abstract]
Hummer G, Szabo A Free energy profiles from single-molecule pulling experiments. Proc Natl Acad Sci USA (107):21441-6, 2010. [PMID: 21098304] [Full text/Abstract]
Zhu F, Hummer G Pore opening and closing of a pentameric ligand-gated ion channel. Proc Natl Acad Sci USA (107):19814-9, 2010. [PMID: 21041674] [Full text/Abstract]
Yin H, Feng G, Clore GM, Hummer G, Rasaiah JC Water in the polar and nonpolar cavities of the protein interleukin-1β. J Phys Chem B (114):16290-7, 2010. [PMID: 21047091] [Full text/Abstract]
Kalra A, Garde S, Hummer G Lubrication by molecularly thin water films confined between nanostructured membranes. Eur Phys J(189):147-54, 2010. [Full text/Abstract]
Hummer G Molecular binding: under water’s influence. Nature Chemistry (2):906-7, 2010. [PMID: 20966940] [Full text/Abstract]
Mittal J, Hummer G Interfacial thermodynamics of confined water near molecularly rough surfaces. Faraday Discuss (146):341-52, 2010. [PMID: 21043431] [Full text/Abstract]
Best RB, Hummer G Coordinate-dependent diffusion in protein folding. Proc Natl Acad Sci USA (107):1088-93, 2010. [PMCID: PMC2824289] [Full text/Abstract]
Rosta E, Hummer G Error and efficiency of simulated tempering simulations. J Chem Phys (132):034102, 2010. [PMID: 19894977] [Full text/Abstract]
Hummer G Catching a protein in the act. Proc Natl Acad Sci USA (107):2381-2, 2010 [PMCID: PMC2823913] [Full text/Abstract]
Kim YC, Furchtgott L, Hummer G Biological proton pumping in an oscillating electric field. Phys Rev Lett (103):268102, 2009. [PMID: 20366348] [Full text/Abstract]
Zhu FQ, Hummer G Gating Transition of Pentameric Ligand-Gated Ion Channels. Biophysical Journal (97):2456-63, 2009. [Full text/Abstract]
Rosta E, Hummer G Error and efficiency of replica exchange molecular dynamics simulations. Journal of Chemical Physics (131):165102, 2009. [Full text /Abstract]
Frewen TA, Hummer G, Kevrekidis IG Exploration of effective potential landscapes using coarse reverse integration. Journal of Chemical Physics (131):134104, 2009. [Full text /Abstract]
Kim YC, Wikström M, Hummer G Kinetic gating of the proton pump in cytochrome c oxidase. Proceedings of the National Academy of Sciences USA (106):13707-12, 2009. [Full text /Abstract ]
Kaila VRI, Verkhovsky MI, Hummer G, Wikström M Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase. Biochimica et Biophysica Acta-Bioenergetics (1787):1205-14, 2009. [Full text /Abstract]
Best RB, Hummer G Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides. Journal of Physical Chemistry B (113):9004-15, 2009. [Full text /Abstract]
Rosta E, Woodcock HL, Brooks BR, Hummer G. Artificial Reaction Coordinate "Tunneling" in Free-Energy Calculations: The Catalytic Reaction of RNase H. Journal of Computational Chemistry (30):1634-41, 2009. [Full text /Abstract]
Berezhkovskii A, Hummer G, Szabo A Reactive flux and folding pathways in network models of coarse-grained protein dynamics. Journal of Chemical Physics(130):205102, 2009. [Full text /Abstract]
Turjanski AG, Hummer G, Gutkind JS How Mitogen-Activated Protein Kinases Recognize and Phosphorylate Their Targets: A QM/MM Study. Journal Of The American Chemical Society(131): 6141-8, 2009. [Full text/Abstract]
Rosta E, Buchete NV, Hummer G Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations. Journal of Chemical Theory and Computation (5):1393-9, 2009. [Full text/Abstract]
Köfinger J, Hummer G, Dellago, C A one-dimensional dipole lattice model for water in narrow nanopores. Journal of Chemical Physics(130):154110, 2009. [Full text/Abstract]
Ren XF, Kloer DP, Kim YC, Ghirlando R, Saidi LF, Hummer G, Hurley JH Hybrid Structural Model of the Complete Human ESCRT-0 Complex. Structure (17):406-16, 2009. [Full text/Abstract]
Best RB, Hummer G Unfolding the secrets of calmodulin. Science(323):593-4, 2009 [Summary ; Full Text ]
Mittal J, Hummer G Static and dynamic correlations in water at hydrophobic interfaces. Proc Natl Acad Sci U S A(105):20130-5. 2008.
Best RB, Buchete NV, Hummer G Are current molecular dynamics force fields too helical? Biophys J(95): L07-9, 2008. [Full Text/Abstract]
Tikhonova IG, Best RB, Engel S, Gershengorn MC, Hummer G, Costanzi S Atomistic insights into rhodopsin activation from a dynamic model. J Am Chem Soc(130): 10141-9, 2008. [Full Text/Abstract]
Turjanski AG, Gutkind JS, Best RB, Hummer G Binding-induced folding of a natively unstructured transcription factor. PLoS Comput Biol(4): e1000060, 2008. [Full Text/Abstract]
Buchete NV, Hummer G Coarse Master Equations for Peptide Folding Dynamics. J Phys Chem B: 112(19):6057-69, 2008. [Full Text/Abstract]
Kim YC, Hummer G Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. J Mol Biol(375): 1416-33, 2008. [Full Text/Abstract]
Canagarajah BJ, Hummer G, Prinz WA, Hurley JH Dynamics of Cholesterol Exchange in the Oxysterol Binding Protein Family. J Mol Biol: 378(3):737-48, 2008. [Full Text/Abstract]
Kaila VR, Verkhovsky MI, Hummer G, Wikstrom M Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase. Proc Natl Acad Sci U S A(105): 6255-9, 2008. [Full Text/Abstract]
Mittal J, Truskett TM, Errington JR, Hummer G Layering and position-dependent diffusive dynamics of confined fluids. Phys Rev Lett(100): 145901, 2008. [Full Text/Abstract]
Kofinger J, Hummer G, Dellago C Macroscopically ordered water in nanopores. Proc Natl Acad Sci U S A(105): 13218-22, 2008. [Full Text/Abstract]
Buchete NV, Hummer G Peptide folding kinetics from replica exchange molecular dynamics Physical Review E(77): 030902, 2008. [Full Text/Abstract]
Kaila VR, Verkhovsky M, Hummer G, Wikstrom M Prevention of leak in the proton pump of cytochrome c oxidase. Biochim Biophys Acta(1777): 890-2, 2008. [Full Text/Abstract]
Best RB, Hummer G Protein folding kinetics under force from molecular simulation. J Am Chem Soc(130): 3706-7, 2008. [Full Text/Abstract]
Best RB, Paci E, Hummer G, Dudko OK Pulling Direction as a Reaction Coordinate for the Mechanical Unfolding of Single Molecules. J Phys Chem B: 112(19):5968-76, 2008. [Full Text/Abstract]
Kim YC, Tang C, Clore GM, Hummer G Replica exchange simulations of transient encounter complexes in protein-protein association. Proc Natl Acad Sci U S A(105): 12855-60, 2008. [Full Text/Abstract]
Dudko OK, Hummer G, Szabo A Theory, analysis, and interpretation of single-molecule force spectroscopy experiments. Proc Natl Acad Sci U S A(105): 15755-60, 2008. [Full Text/Abstract]
Rasaiah JC, Garde S, Hummer G Water in Nonpolar Confinement: From Nanotubes to Proteins and Beyond. Annu Rev Phys Chem: 59:713-40, 2008. [Full Text/Abstract]
Tuukkanen A, Kaila VR, Laakkonen L, Hummer G, Wikstrom M Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase. Biochim Biophys Acta, 2007. [Full Text/Abstract]
Dudko OK, Mathe J, Szabo A, Meller A, Hummer G Extracting Kinetics from Single-Molecule Force Spectroscopy: Nanopore Unzipping of DNA Hairpins. Biophys J(92): 4188-4195, 2007. [Full Text/Abstract]
Kim YC, Wikstrom M, Hummer G Kinetic models of redox-coupled proton pumping. Proc Natl Acad Sci U S A (104): 2169-74, 2007. [Full Text/Abstract]
Yin H, Hummer G, Rasaiah JC Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion. J Am Chem Soc(129): 7369-77, 2007. [Full Text/Abstract]
Zheng W, Brooks BR, Hummer G Protein conformational transitions explored by mixed elastic network models. Proteins(69): 43-57, 2007. [Full Text/Abstract]
Chen YG, Hummer G Slow Conformational Dynamics and Unfolding of the Calmodulin C-Terminal Domain. J Am Chem Soc(129): 2414 -2415, 2007. [Full Text/Abstract]
Collins MD, Quillin ML, Hummer G, Matthews BW, Gruner SM Structural Rigidity of a Large Cavity-containing Protein Revealed by High-pressure Crystallography J Mol Biol(367): 752-763, 2007. [Full Text/Abstract]
Buchete NV, Hummer G Structure and Dynamics of Parallel beta-Sheets, Hydrophobic Core, and Loops in Alzheimer's A-beta Fibrils. Biophys J(92): 3032-9, 2007. [Full Text/Abstract]
Milac AL, Buchete NV, Fritz TA, Hummer G, Tabak LA Substrate-induced Conformational Changes and Dynamics of UDP-N-Acetylgalactosamine:Polypeptide N-Acetylgalactosaminyltransferase-2. J Mol Biol, 2007. [Full Text/Abstract]
Prag G, Watson H, Kim YC, Beach BM, Ghirlando R, Hummer G, Bonifacino JS, Hurley JH The Vps27/Hse1 Complex Is a GAT Domain-Based Scaffold for Ubiquitin-Dependent Sorting. Dev Cell(12): 973-86, 2007. [Full Text/Abstract]
Hummer G Water pulls the strings in hydrophobic polymer collapse. Proc Natl Acad Sci U S A(104): 14883-4, 2007. [Full Text/Abstract]
Hummer G Water, proton, and ion transport: from nanotubes to proteins Molec. Phys.(105): 201-207, 2007. [Full Text/Abstract]
Best RB, Hummer G Diffusive model of protein folding dynamics with kramers turnover in rate. Phys Rev Lett (96): 228104, 2006. [Full Text/Abstract]
Hassan SA, Hummer G, Lee YS Effects of electric fields on proton transport through water chains. J Chem Phys (124): 204510, 2006. [Full Text/Abstract]
Berezhkovskii AM, Hummer G, Bezrukov SM Identity of Distributions of Direct Uphill and Downhill Translocation Times for Particles Traversing Membrane Channels Phys Rev Lett(97): 020601, 2006. [Full Text/Abstract]
Dudko OK, Hummer G, Szabo A Intrinsic rates and activation free energies from single-molecule pulling experiments. Phys Rev Lett (96): 108101, 2006. [Full Text/Abstract]
Dellago C, Hummer G Kinetics and mechanism of proton transport across membrane nanopores. Phys Rev Lett (97): 245901, 2006. [Full Text/Abstract]
Sriraman S, Kevrekidis IG, Hummer G Coarse master equation from Bayesian analysis of replica molecular dynamics simulations J. Phys. Chem. B(109): 6479-6484, 2005. [Full Text/Abstract]
Sriraman S, Kevrekidis IG, Hummer G Coarse Nonlinear Dynamics and Metastability of Filling-Emptying Transitions: Water in Carbon Nanotubes Phys. Rev. Lett.(95): 130603, 2005. [Full Text/Abstract]
Best RB, Hummer G Comment on "Force-clamp spectroscopy monitors the folding trajectory of a single protein" Science(308): 498, 2005. [Full Text/Abstract]
Collins MD, Hummer G, Quillin ML, Matthews BW, Gruner SM Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation. Proc Natl Acad Sci U S A (102): 16668-16671, 2005. [Full Text/Abstract]
Gustchina E, Hummer G, Bewley CA, Clore GM 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. J Med Chem (48): 3036-44, 2005. [Full Text/Abstract]
Andreev S, Reichman D, Hummer G Effect of flexibility on hydrophobic behavior of nanotube water channels. J Chem Phys (123): 194502, 2005. [Full Text/Abstract]
Hummer G, Szabo A Free energy surfaces from single-molecule force spectroscopy. Acc Chem Res (38): 504-13, 2005. [Full Text/Abstract]
Peter C, Hummer G Ion Transport through Membrane-Spanning Nanopores Studied by Molecular Dynamics Simulations and Continuum Electrostatics Calculations. Biophys J (89): 2222-34, 2005. [Full Text/Abstract]
Buchete NV, Tycko R, Hummer G Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments. J Mol Biol(353): 804-21, 2005. [Full Text/Abstract]
Hummer G Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations New Journal of Physics(7): 34, 2005. [Full Text/Abstract]
Best RB, Hummer G Reaction coordinates and rates from transition paths. Proc Natl Acad Sci U S A(102): 6732-6737, 2005. [Full Text/Abstract]
Best RB, Chen YG, Hummer G Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressor. Structure (Camb) (13): 1755-63, 2005. [Full Text/Abstract]
Yeh IC, Hummer G Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations. Biophys J (86): 681-9, 2004. [Full Text/Abstract]
Vaitheeswaran S, Rasaiah JC, Hummer G Electric field and temperature effects on water in the narrow nonpolar pores of carbon nanotubes. J Chem Phys (121): 7955-65, 2004. [Full Text/Abstract]
Kevrekidis IG, Gear CW, Hummer G Equation-free: The computer-aided analysis of complex multiscale systems AIChE J.(50): 1346-55, 2004.
Hummer G From transition paths to transition states and rate coefficients. J Chem Phys (120): 516-23, 2004. [Full Text/Abstract]
Kalra A, Garde S, Hummer G Methane partitioning and transport in hydrated carbon nanotubes J. Phys. Chem. B(108): 544-9, 2004.