Journal Article (370)
2012
Journal Article
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 109 (47), pp. 19256 - 19261 (2012)
Journal Article
Theory and simulation of ion conduction in the pentameric GLIC channel. Journal of Chemical Theory and Computation 8 (10), pp. 3759 - 3768 (2012)
Journal Article
Membrane-elasticity model of Coatless vesicle budding induced by ESCRT complexes. PLoS Computational Biology 8 (10), e1002736 (2012)
Journal Article
Transition path times for DNA and RNA folding from force spectroscopy. Physics 5, 87 (2012)
Journal Article
Pair diffusion, hydrodynamic interactions, and available volume in dense fluids. The Journal of Chemical Physics 137 (3), 034110 (2012)
Journal Article
Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction. Biophysical Journal 103 (2), pp. 219 - 227 (2012)
Journal Article
Characterization of a dynamic string method for the construction of transition pathways in molecular reactions. The Journal of Physical Chemistry B 116 (29), pp. 8573 - 8583 (2012)
Journal Article
Entropy of single-file water in (6,6) carbon nanotubes. The Journal of Chemical Physics 137 (4), 044709 (2012)
Journal Article
Solution structure of the ESCRT-I and -II supercomplex: implications for membrane budding and scission. Structure 20 (5), pp. 874 - 886 (2012)
Journal Article
Proton-pumping mechanism of cytochrome c oxidase: a kinetic master-equation approach. Biochimica et Biophysica Acta: BBA 1817 (4), pp. 526 - 536 (2012)
Journal Article
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 109 (12), pp. 4431 - 4436 (2012)
Journal Article
Convergence and error estimation in free energy calculations using the weighted histogram analysis method. Journal of Computational Chemistry 33 (4), pp. 453 - 465 (2012)
2011
Journal Article
Structural basis of p38α regulation by hematopoietic tyrosine phosphatase. Nature Chemical Biology 7 (12), pp. 916 - 924 (2011)
Journal Article
Resting and active states of the ERK2:HePTP complex. Journal of the American Chemical Society 133 (43), pp. 17138 - 17141 (2011)
Journal Article
Energetics of direct and water-mediated proton-coupled electron transfer. Journal of the American Chemical Society 133 (47), pp. 19040 - 19043 (2011)
Journal Article
Diffusion models of protein folding. Physical Chemistry Chemical Physics 13 (38), pp. 16902 - 16911 (2011)
Journal Article
Single-file water in nanopores. Physical Chemistry Chemical Physics 13 (34), pp. 15403 - 15417 (2011)
Journal Article
Energetics and dynamics of proton transfer reactions along short water wires. Physical Chemistry Chemical Physics 13 (29), pp. 13207 - 13215 (2011)
Journal Article
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 108 (23), pp. 9437 - 9442 (2011)
Journal Article
Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations. Journal of the American Chemical Society 133 (23), pp. 8934 - 8941 (2011)
Journal Article
SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions. Structure 19 (1), pp. 109 - 116 (2011)
Journal Article
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 108 (2), pp. 603 - 608 (2011)
Journal Article
Crystal structure and allosteric activation of protein kinase C βII. Cell 144 (1), pp. 55 - 66 (2011)
2010
Journal Article
Water in the polar and nonpolar cavities of the protein interleukin-1β. The Journal of Physical Chemistry B 114 (49), pp. 16290 - 16297 (2010)
Journal Article
Free energy profiles from single-molecule pulling experiments. Proceedings of the National Academy of Sciences of the United States of America 107 (50), pp. 21441 - 21446 (2010)
Journal Article
Pore opening and closing of a pentameric ligand-gated ion channel. Proceedings of the National Academy of Sciences of the United States of America 107 (46), pp. 19814 - 19819 (2010)
Journal Article
Under water's influence. Nature Chemistry 2 (11), pp. 906 - 907 (2010)
Journal Article
Lubrication by molecularly thin water films confined between nanostructured membranes. The European Physical Journal Special Topics 189 (1), pp. 147 - 154 (2010)
Journal Article
Catching a protein in the act. Proceedings of the National Academy of Sciences of the United States of America 107 (6), pp. 2381 - 2382 (2010)
Journal Article
Error and efficiency of simulated tempering simulations. The Journal of Chemical Physics 132 (3), 034102 (2010)
Journal Article
Coordinate-dependent diffusion in protein folding. Proceedings of the National Academy of Sciences of the United States of America 107 (3), pp. 1088 - 1093 (2010)
Journal Article
Interfacial thermodynamics of confined water near molecularly rough surfaces. Faraday Discussions 146, pp. 341 - 352 (2010)
2009
Journal Article
Biological proton pumping in an oscillating electric field. Physical Review Letters 103 (26), 268102 (2009)
Journal Article
Gating transition of pentameric ligand-gated ion channels. Biophysical Journal (Annual Meeting Abstracts) 97 (9), pp. 2456 - 2463 (2009)
Journal Article
Error and efficiency of replica exchange molecular dynamics simulations. The Journal of Chemical Physics 131 (16), 165102 (2009)
Journal Article
Exploration of effective potential landscapes using coarse reverse integration. The Journal of Chemical Physics 131 (13), 134104 (2009)
Journal Article
Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase. Biochimica et Biophysica Acta (BBA) - General Subjects 1787 (10), pp. 1205 - 1214 (2009)
Journal Article
Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H. Journal of Computational Chemistry 30 (11), pp. 1634 - 1641 (2009)
Journal Article
Kinetic gating of the proton pump in cytochrome c oxidase. Proceedings of the National Academy of Sciences of the United States of America 106 (33), pp. 13707 - 13712 (2009)
Journal Article
Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. The Journal of Physical Chemistry B 113 (26), pp. 9004 - 9015 (2009)
Journal Article
Reactive flux and folding pathways in network models of coarse-grained protein dynamics. The Journal of Chemical Physics 130 (20), 205102 (2009)
Journal Article
How mitogen-activated protein kinases recognize and phosphorylate their targets: A QM/MM study. Journal of the American Chemical Society 131 (17), pp. 6141 - 6148 (2009)
Journal Article
A one-dimensional dipole lattice model for water in narrow nanopores. The Journal of Chemical Physics 130 (15), 154110 (2009)
Journal Article
Hybrid structural model of the complete human ESCRT-0 complex. Structure 17 (3), pp. 406 - 416 (2009)
Journal Article
Unfolding the secrets of calmodulin. Science 323 (5914), pp. 593 - 594 (2009)
Journal Article
Thermostat artifacts in replica exchange molecular dynamics simulations. Journal of Chemical Theory and Computation 5 (5), pp. 1393 - 1399 (2009)
2008
Journal Article
Static and dynamic correlations in water at hydrophobic interfaces. Proceedings of the National Academy of Sciences of the United States of America 105 (51), pp. 20130 - 20135 (2008)
Journal Article
Theory, analysis, and interpretation of single-molecule force spectroscopy experiments. Proceedings of the National Academy of Sciences of the United States of America 105 (41), pp. 15755 - 15760 (2008)
Journal Article
Macroscopically ordered water in nanopores. Proceedings of the National Academy of Sciences of the United States of America 105 (36), pp. 13218 - 13222 (2008)
Journal Article
Replica exchange simulations of transient encounter complexes in protein-protein association. Proceedings of the National Academy of Sciences of the United States of America 105 (35), pp. 12855 - 12860 (2008)
Journal Article
Atomistic insights into rhodopsin activation from a dynamic model. Journal of the American Chemical Society 130 (31), pp. 10141 - 10149 (2008)
Journal Article
Prevention of leak in the proton pump of cytochrome c oxidase. Biochimica et Biophysica Acta (BBA) - General Subjects 1777 (7-8), pp. 890 - 892 (2008)
Journal Article
Are current molecular dynamics force fields too helical? Biophysical Journal 95 (1), pp. L07 - L09 (2008)
Journal Article
A tribute to Attila Szabo. The Journal of Physical Chemistry B 112 (19), pp. 5881 - 5882 (2008)
Journal Article
Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules. The Journal of Physical Chemistry B 112 (19), pp. 5968 - 5976 (2008)
Journal Article
Coarse master equations for peptide folding dynamics. The Journal of Physical Chemistry B 112 (19), pp. 6057 - 6069 (2008)
Journal Article
Dynamics of cholesterol exchange in the oxysterol binding protein family. Journal of Molecular Biology 378 (3), pp. 737 - 748 (2008)
Journal Article
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 105 (17), pp. 6255 - 6259 (2008)
Journal Article
Layering and position-dependent diffusive dynamics of confined fluids. Physical Review Letters 100 (14), p. 145901 (4) (2008)
Journal Article
Binding-induced folding of a natively unstructured transcription factor. PLoS Computational Biology 4 (4), e1000060 (2008)
Journal Article
Protein folding kinetics under force from molecular simulation. Journal of the American Chemical Society 130 (12), pp. 3706 - 3707 (2008)
Journal Article
Peptide folding kinetics from replica exchange molecular dynamics. Physical Review E 77 (3 Pt 1), pp. 030902-1 - 030902-4 (2008)
Journal Article
Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. Journal of Molecular Biology (London) 375 (5), pp. 1416 - 1433 (2008)
2007
Journal Article
Substrate-induced conformational changes and dynamics of UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferase-2. Journal of Molecular Biology 373 (2), pp. 439 - 451 (2007)
Journal Article
Protein conformational transitions explored by mixed elastic network models. Proteins: Structure, Function, and Bioinformatics 69 (1), pp. 43 - 57 (2007)
Journal Article
Water pulls the strings in hydrophobic polymer collapse. Proceedings of the National Academy of Sciences of the United States of America 104 (38), pp. 14883 - 14884 (2007)
Journal Article
Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase. Biochimica et Biophysica Acta: BBA 1767 (9), pp. 1102 - 1106 (2007)
Journal Article
Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins. Biophysical Journal (Annual Meeting Abstracts) 92 (12), pp. 4188 - 4195 (2007)
Journal Article
Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion. Journal of the American Chemical Society 129 (23), pp. 7369 - 7377 (2007)
Journal Article
The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting. Developmental Cell 12 (6), pp. 973 - 986 (2007)
Journal Article
Structure and dynamics of parallel beta-sheets, hydrophobic core, and loops in Alzheimer's A beta fibrils. Biophysical Journal (Annual Meeting Abstracts) 92 (9), pp. 3032 - 3039 (2007)
Journal Article
Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography. Journal of Molecular Biology (London) 367 (3), pp. 752 - 763 (2007)
Journal Article
Slow conformational dynamics and unfolding of the calmodulin C-terminal domain. Journal of the American Chemical Society 129 (9), pp. 2414 - 2415 (2007)
Journal Article
Kinetic models of redox-coupled proton pumping. Proceedings of the National Academy of Sciences of the United States of America 104 (7), pp. 2169 - 2174 (2007)
Journal Article
Water, proton, and ion transport: from nanotubes to proteins. Molecular Physics 105 (2-3), pp. 201 - 207 (2007)
2006
Journal Article
Kinetics and mechanism of proton transport across membrane nanopores. Physical Review Letters 97 (24), 245901 (2006)
Journal Article
Identity of distributions of direct uphill and downhill translocation times for particles traversing membrane channels. Physical Review Letters 97 (2), 020601 (2006)
Journal Article
Identity of distributions of direct uphill and downhill translocation times for particles traversing membrane channels. Physical Review Letters 97 (2), 020601 (2006)
Journal Article
Diffusive model of protein folding dynamics with Kramers turnover in rate. Physical Review Letters 96 (22), 228104 (2006)
Journal Article
Effects of electric fields on proton transport through water chains. The Journal of Chemical Physics 124 (20), 204510 (2006)
Journal Article
Intrinsic rates and activation free energies from single-molecule pulling experiments. Physical Review Letters 96 (10), 108101 (2006)
2005
Journal Article
Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressor. Structure 13 (12), pp. 1755 - 1763 (2005)
Journal Article
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 102 (46), pp. 16668 - 16671 (2005)
Journal Article
Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments. Journal of Molecular Biology (London) 353 (4), pp. 804 - 821 (2005)
Journal Article
Effect of flexibility on hydrophobic behavior of nanotube water channels. The Journal of Chemical Physics 123 (19), 194502 (2005)
Journal Article
Ion transport through membrane-spanning nanopores studied by molecular dynamics simulations and continuum electrostatics calculations. Biophysical Journal 89 (4), pp. 2222 - 2234 (2005)
Journal Article
Ion Transport through Membrane-Spanning Nanopores Studiedby Molecular Dynamics Simulations and ContinuumElectrostatics Calculations. Biophysical Journal 89, pp. 2222 - 2234 (2005)
Journal Article
Coarse nonlinear dynamics and metastability of filling-emptying transitions: water in carbon nanotubes. Physical Review Letters 95 (13), 130603 (2005)
Journal Article
Coarse nonlinear dynamics and metastability of filling-emptying transitions: water in carbon nanotubes. Physical Review Letters 95 (13), 130603 (2005)
Journal Article
Free energy surfaces from single-molecule force spectroscopy. Accounts of Chemical Research 38 (7), pp. 504 - 513 (2005)
Journal Article
Reaction coordinates and rates from transition paths. Proceedings of the National Academy of Sciences of the United States of America 102 (19), pp. 6732 - 6737 (2005)
Journal Article
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 48 (8), pp. 3036 - 3044 (2005)
Journal Article
Coarse master equation from Bayesian analysis of replica molecular dynamics simulations. The Journal of Physical Chemistry B 109 (14), pp. 6479 - 6484 (2005)
Journal Article
Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations. New Journal of Physics 7, 34 (2005)
2004
Journal Article
Water clusters in nonpolar cavities. Proceedings of the National Academy of Sciences of the United States of America 101 (49), pp. 17002 - 17005 (2004)
Journal Article
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 101 (43), pp. 15330 - 15334 (2004)
Journal Article
Electric field and temperature effects on water in the narrow nonpolar pores of carbon nanotubes. The Journal of Chemical Physics 121 (16), pp. 7955 - 7965 (2004)
Journal Article
System-Size Dependence of Diffusion Coefficients and Viscosities from Molecular Dynamics Simulations with Periodic Boundary Conditions. The Journal of Physical Chemistry B 108 (40), pp. 15873 - 15879 (2004)
Journal Article
Nucleic acid transport through carbon nanotube membranes. Proceedings of the National Academy of Sciences of the United States of America 101 (33), pp. 12177 - 12182 (2004)