1. Best RB, Buchete NV, Hummer G Are current molecular dynamics force fields too helical? Biophys J(95): L07-9, 2008. [Full Text/Abstract]
2. 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]
3. 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]
4. Buchete NV, Hummer G Coarse Master Equations for Peptide Folding Dynamics. J Phys Chem B: 112(19):6057-69, 2008. [Full Text/Abstract]
5. 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]
6. 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]
7. 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]
8. 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]
9. 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]
10. Buchete NV, Hummer G Peptide folding kinetics from replica exchange molecular dynamics Physical Review E(77): 030902, 2008. [Full Text/Abstract]
11. 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]
12. Best RB, Hummer G Protein folding kinetics under force from molecular simulation. J Am Chem Soc(130): 3706-7, 2008. [Full Text/Abstract]
13. 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]
14. 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]
15. 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]
16. 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]
17. 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]
18. 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]
19. 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]
20. 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]
21. Zheng W, Brooks BR, Hummer G Protein conformational transitions explored by mixed elastic network models. Proteins(69): 43-57, 2007. [Full Text/Abstract]
22. 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]
23. 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]
24. 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]
25. 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]
26. 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]
27. Hummer G Water pulls the strings in hydrophobic polymer collapse. Proc Natl Acad Sci U S A(104): 14883-4, 2007. [Full Text/Abstract]
28. Hummer G Water, proton, and ion transport: from nanotubes to proteins Molec. Phys.(105): 201-207, 2007. [Full Text/Abstract]
29. Best RB, Hummer G Diffusive model of protein folding dynamics with kramers turnover in rate. Phys Rev Lett (96): 228104, 2006. [Full Text/Abstract]
30. 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]
31. 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]
32. 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]
33. Dellago C, Hummer G Kinetics and mechanism of proton transport across membrane nanopores. Phys Rev Lett (97): 245901, 2006. [Full Text/Abstract]
34. 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]
35. 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]
36. Best RB, Hummer G Comment on "Force-clamp spectroscopy monitors the folding trajectory of a single protein" Science(308): 498, 2005. [Full Text/Abstract]
37. 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]
38. 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]
39. 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]
40. Hummer G, Szabo A Free energy surfaces from single-molecule force spectroscopy. Acc Chem Res (38): 504-13, 2005. [Full Text/Abstract]
41. 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]
42. 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]
43. 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]
44. 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]
45. 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]
46. 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]
47. 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]
48. Kevrekidis IG, Gear CW, Hummer G Equation-free: The computer-aided analysis of complex multiscale systems AIChE J.(50): 1346-55, 2004.
49. Hummer G From transition paths to transition states and rate coefficients. J Chem Phys (120): 516-23, 2004. [Full Text/Abstract]
50. Kalra A, Garde S, Hummer G Methane partitioning and transport in hydrated carbon nanotubes J. Phys. Chem. B(108): 544-9, 2004.
