-
1
-
-
0023449962
-
Spin glasses and the statistical mechanics of protein folding
-
Bryngelson JD, Wolynes PG (1987) Spin glasses and the statistical mechanics of protein folding. Proc Natl Acad Sci USA 84(21):7524-7528.
-
(1987)
Proc Natl Acad Sci USA
, vol.84
, Issue.21
, pp. 7524-7528
-
-
Bryngelson, J.D.1
Wolynes, P.G.2
-
2
-
-
84869761071
-
The protein-folding problem, 50 years on
-
Dill KA, MacCallum JL (2012) The protein-folding problem, 50 years on. Science 338(6110):1042-1046.
-
(2012)
Science
, vol.338
, Issue.6110
, pp. 1042-1046
-
-
Dill, K.A.1
Maccallum, J.L.2
-
3
-
-
84901982914
-
Reconstructing folding energy landscapes by singlemolecule force spectroscopy
-
Woodside MT, Block SM (2014) Reconstructing folding energy landscapes by singlemolecule force spectroscopy. Annu Rev Biophys 43:19-39.
-
(2014)
Annu Rev Biophys
, vol.43
, pp. 19-39
-
-
Woodside, M.T.1
Block, S.M.2
-
4
-
-
33750970551
-
Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid
-
Woodside MT, et al. (2006) Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid. Science 314(5801):1001-1004.
-
(2006)
Science
, vol.314
, Issue.5801
, pp. 1001-1004
-
-
Woodside, M.T.1
-
5
-
-
76649093956
-
Full distance-resolved folding energy landscape of one single protein molecule
-
Gebhardt JCM, Bornschlögl T, Rief M (2010) Full distance-resolved folding energy landscape of one single protein molecule. Proc Natl Acad Sci USA 107(5):2013-2018.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, Issue.5
, pp. 2013-2018
-
-
Gebhardt, J.C.M.1
Bornschlögl, T.2
Rief, M.3
-
6
-
-
79960305090
-
Measuring the folding landscape of a harmonically constrained biopolymer
-
de Messieres M, Brawn-Cinani B, La Porta A (2011) Measuring the folding landscape of a harmonically constrained biopolymer. Biophys J 100(11):2736-2744.
-
(2011)
Biophys J
, vol.100
, Issue.11
, pp. 2736-2744
-
-
De Messieres, M.1
Brawn-Cinani, B.2
La Porta, A.3
-
7
-
-
79960978673
-
Reconstructing free energy profiles from nonequilibrium relaxation trajectories
-
Zhang Q, Brujic J, Vanden-Eijnden E (2011) Reconstructing free energy profiles from nonequilibrium relaxation trajectories. J Stat Phys 144(2):344-366.
-
(2011)
J Stat Phys
, vol.144
, Issue.2
, pp. 344-366
-
-
Zhang, Q.1
Brujic, J.2
Vanden-Eijnden, E.3
-
8
-
-
84875438723
-
Force-clamp experiments reveal the free-energy profile and diffusion coefficient of the collapse of protein molecules
-
Lannon H, Haghpanah JS, Montclare JK, Vanden-Eijnden E, Brujic J (2013) Force-clamp experiments reveal the free-energy profile and diffusion coefficient of the collapse of protein molecules. Phys Rev Lett 110(12):128301.
-
(2013)
Phys Rev Lett
, vol.110
, Issue.12
, pp. 128301
-
-
Lannon, H.1
Haghpanah, J.S.2
Montclare, J.K.3
Vanden-Eijnden, E.4
Brujic, J.5
-
9
-
-
0035957434
-
Free energy reconstruction from nonequilibrium singlemolecule pulling experiments
-
Hummer G, Szabo A (2001) Free energy reconstruction from nonequilibrium singlemolecule pulling experiments. Proc Natl Acad Sci USA 98(7):3658-3661.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, Issue.7
, pp. 3658-3661
-
-
Hummer, G.1
Szabo, A.2
-
10
-
-
78650753691
-
Free energy profiles from single-molecule pulling experiments
-
Hummer G, Szabo A (2010) Free energy profiles from single-molecule pulling experiments. Proc Natl Acad Sci USA 107(50):21441-21446.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, Issue.50
, pp. 21441-21446
-
-
Hummer, G.1
Szabo, A.2
-
11
-
-
79961021741
-
Experimental validation of free-energy-landscape reconstruction from non-equilibrium single-molecule force spectroscopy measurements
-
Gupta AN, et al. (2011) Experimental validation of free-energy-landscape reconstruction from non-equilibrium single-molecule force spectroscopy measurements. Nat Phys 7(8): 631-634.
-
(2011)
Nat Phys
, vol.7
, Issue.8
, pp. 631-634
-
-
Gupta, A.N.1
-
12
-
-
84875249565
-
From mechanical folding trajectories to intrinsic energy landscapes of biopolymers
-
Hinczewski M, Gebhardt JCM, Rief M, Thirumalai D (2013) From mechanical folding trajectories to intrinsic energy landscapes of biopolymers. Proc Natl Acad Sci USA 110(12):4500-4505.
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, Issue.12
, pp. 4500-4505
-
-
Hinczewski, M.1
Gebhardt, J.C.M.2
Rief, M.3
Thirumalai, D.4
-
13
-
-
84908170803
-
Determining intrachain diffusion coefficients for biopolymer dynamics from single-molecule force spectroscopy measurements
-
Woodside MT, Lambert J, Beach KSD (2014) Determining intrachain diffusion coefficients for biopolymer dynamics from single-molecule force spectroscopy measurements. Biophys J 107(7):1647-1653.
-
(2014)
Biophys J
, vol.107
, Issue.7
, pp. 1647-1653
-
-
Woodside, M.T.1
Lambert, J.2
Beach, K.S.D.3
-
14
-
-
0001563395
-
On the transition coordinate for protein folding
-
Du R, Pande VS, Grosberg AY, Tanaka T, Shakhnovich ES (1998) On the transition coordinate for protein folding. J Chem Phys 108(1):334-350.
-
(1998)
J Chem Phys
, vol.108
, Issue.1
, pp. 334-350
-
-
Du, R.1
Pande, V.S.2
Grosberg, A.Y.3
Tanaka, T.4
Shakhnovich, E.S.5
-
15
-
-
33646587736
-
Nanomechanical measurements of the sequencedependent folding landscapes of single nucleic acid hairpins
-
Woodside MT, et al. (2006) Nanomechanical measurements of the sequencedependent folding landscapes of single nucleic acid hairpins. Proc Natl Acad Sci USA 103(16):6190-6195.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.16
, pp. 6190-6195
-
-
Woodside, M.T.1
-
16
-
-
80052003642
-
Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments
-
Chodera JD, Pande VS (2011) Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments. Phys Rev Lett 107(9):098102.
-
(2011)
Phys Rev Lett
, vol.107
, Issue.9
, pp. 098102
-
-
Chodera, J.D.1
Pande, V.S.2
-
17
-
-
17444378255
-
One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability distribution
-
Rhee YM, Pande VS (2005) One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability distribution. J Phys Chem B 109(14):6780-6786.
-
(2005)
J Phys Chem B
, vol.109
, Issue.14
, pp. 6780-6786
-
-
Rhee, Y.M.1
Pande, V.S.2
-
18
-
-
75749153687
-
Coordinate-dependent diffusion in protein folding
-
Best RB, Hummer G (2010) Coordinate-dependent diffusion in protein folding. Proc Natl Acad Sci USA 107(3):1088-1093.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, Issue.3
, pp. 1088-1093
-
-
Best, R.B.1
Hummer, G.2
-
19
-
-
33847254454
-
Ultrafast dynamics of protein collapse from single-molecule photon statistics
-
Nettels D, Gopich IV, Hoffmann A, Schuler B (2007) Ultrafast dynamics of protein collapse from single-molecule photon statistics. Proc Natl Acad Sci USA 104(8):2655-2660.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, Issue.8
, pp. 2655-2660
-
-
Nettels, D.1
Gopich, I.V.2
Hoffmann, A.3
Schuler, B.4
-
20
-
-
57449106823
-
Chemical, physical, and theoretical kinetics of an ultrafast folding protein
-
Kubelka J, Henry ER, Cellmer T, Hofrichter J, Eaton WA (2008) Chemical, physical, and theoretical kinetics of an ultrafast folding protein. Proc Natl Acad Sci USA 105(48): 18655-18662.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.48
, pp. 18655-18662
-
-
Kubelka, J.1
Henry, E.R.2
Cellmer, T.3
Hofrichter, J.4
Eaton, W.A.5
-
21
-
-
84862076708
-
Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy
-
Soranno A, et al. (2012) Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy. Proc Natl Acad Sci USA 109(44): 17800-17806.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.44
, pp. 17800-17806
-
-
Soranno, A.1
-
22
-
-
33744768052
-
Force-dependent fragility in RNA hairpins
-
Manosas M, Collin D, Ritort F (2006) Force-dependent fragility in RNA hairpins. Phys Rev Lett 96(21):218301.
-
(2006)
Phys Rev Lett
, vol.96
, Issue.21
, pp. 218301
-
-
Manosas, M.1
Collin, D.2
Ritort, F.3
-
23
-
-
28844460238
-
Passive all-optical force clamp for high-resolution laser trapping
-
Greenleaf WJ, Woodside MT, Abbondanzieri EA, Block SM (2005) Passive all-optical force clamp for high-resolution laser trapping. Phys Rev Lett 95(20):208102.
-
(2005)
Phys Rev Lett
, vol.95
, Issue.20
, pp. 208102
-
-
Greenleaf, W.J.1
Woodside, M.T.2
Abbondanzieri, E.A.3
Block, S.M.4
-
24
-
-
79960622883
-
Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments
-
Morrison G, Hyeon C, Hinczewski M, Thirumalai D (2011) Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments. Phys Rev Lett 106(13):138102.
-
(2011)
Phys Rev Lett
, vol.106
, Issue.13
, pp. 138102
-
-
Morrison, G.1
Hyeon, C.2
Hinczewski, M.3
Thirumalai, D.4
-
25
-
-
84925261006
-
Transition-path probability as a test of reaction-coordinate quality reveals DNA hairpin folding is a one-dimensional diffusive process
-
Neupane K, Manuel AP, Lambert J, Woodside MT (2015) Transition-path probability as a test of reaction-coordinate quality reveals DNA hairpin folding is a one-dimensional diffusive process. J Phys Chem Lett 6(6):1005-1010.
-
(2015)
J Phys Chem Lett
, vol.6
, Issue.6
, pp. 1005-1010
-
-
Neupane, K.1
Manuel, A.P.2
Lambert, J.3
Woodside, M.T.4
-
26
-
-
84255177954
-
Signal-pair correlation analysis of single-molecule trajectories
-
Hoffmann A, Woodside MT (2011) Signal-pair correlation analysis of single-molecule trajectories. Angew Chem Int Ed Engl 50(52):12643-12646.
-
(2011)
Angew Chem Int Ed Engl
, vol.50
, Issue.52
, pp. 12643-12646
-
-
Hoffmann, A.1
Woodside, M.T.2
-
28
-
-
0018101150
-
Models for the specific adhesion of cells to cells
-
Bell GI (1978) Models for the specific adhesion of cells to cells. Science 200(4342): 618-627.
-
(1978)
Science
, vol.200
, Issue.4342
, pp. 618-627
-
-
Bell, G.I.1
-
29
-
-
84873050143
-
Effect of handle length and microsphere size on transition kinetics in single-molecule experiments
-
Chang J-C, de Messieres M, La Porta A (2013) Effect of handle length and microsphere size on transition kinetics in single-molecule experiments. Phys Rev E Stat Nonlin Soft Matter Phys 87(1):012721.
-
(2013)
Phys Rev e Stat Nonlin Soft Matter Phys
, vol.87
, Issue.1
, pp. 012721
-
-
Chang, J.-C.1
De Messieres, M.2
La Porta, A.3
-
30
-
-
84919740905
-
Communication: Does force spectroscopy of biomolecules probe their intrinsic dynamic properties?
-
Makarov DE (2014) Communication: Does force spectroscopy of biomolecules probe their intrinsic dynamic properties? J Chem Phys 141(24):241103.
-
(2014)
J Chem Phys
, vol.141
, Issue.24
, pp. 241103
-
-
Makarov, D.E.1
-
31
-
-
81055126961
-
Locating the barrier for folding of single molecules under an external force
-
Dudko OK, Graham TGW, Best RB (2011) Locating the barrier for folding of single molecules under an external force. Phys Rev Lett 107(20):208301.
-
(2011)
Phys Rev Lett
, vol.107
, Issue.20
, pp. 208301
-
-
Dudko, O.K.1
Graham, T.G.W.2
Best, R.B.3
-
32
-
-
18744387720
-
Reaction coordinates and rates from transition paths
-
Best RB, Hummer G (2005) Reaction coordinates and rates from transition paths. Proc Natl Acad Sci USA 102(19):6732-6737.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, Issue.19
, pp. 6732-6737
-
-
Best, R.B.1
Hummer, G.2
-
33
-
-
57349124448
-
Theory, analysis, and interpretation of singlemolecule force spectroscopy experiments
-
Dudko OK, Hummer G, Szabo A (2008) Theory, analysis, and interpretation of singlemolecule force spectroscopy experiments. Proc Natl Acad Sci USA 105(41):15755-15760.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.41
, pp. 15755-15760
-
-
Dudko, O.K.1
Hummer, G.2
Szabo, A.3
-
34
-
-
0347193736
-
Reaction-rate theory-50 years after Kramers
-
Hanggi P, Talkner P, Borkovec M (1990) Reaction-rate theory-50 years after Kramers. Rev Mod Phys 62(2):251-341.
-
(1990)
Rev Mod Phys
, vol.62
, Issue.2
, pp. 251-341
-
-
Hanggi, P.1
Talkner, P.2
Borkovec, M.3
-
35
-
-
84864661883
-
Transition path times for nucleic Acid folding determined from energy-landscape analysis of single-molecule trajectories
-
Neupane K, et al. (2012) Transition path times for nucleic Acid folding determined from energy-landscape analysis of single-molecule trajectories. Phys Rev Lett 109(6): 068102.
-
(2012)
Phys Rev Lett
, vol.109
, Issue.6
, pp. 068102
-
-
Neupane, K.1
-
36
-
-
84880316740
-
A simple and effective Verlet-type algorithm for simulating Langevin dynamics
-
Gronbech-Jensen N, Farago O (2013) A simple and effective Verlet-type algorithm for simulating Langevin dynamics. Mol Phys 111(8):983-991.
-
(2013)
Mol Phys
, vol.111
, Issue.8
, pp. 983-991
-
-
Gronbech-Jensen, N.1
Farago, O.2
|