-
1
-
-
34347266453
-
High-Resolution, Single-Molecule Measurements of Biomolecular Motion
-
W. J. Greenleaf, M. T. Woodside, and S. M. Block, High-Resolution, Single-Molecule Measurements of Biomolecular Motion, Annu. Rev. Biophys. Biomol. Struct. 36, 171 (2007).
-
(2007)
Annu. Rev. Biophys. Biomol. Struct.
, vol.36
, pp. 171
-
-
Greenleaf, W.J.1
Woodside, M.T.2
Block, S.M.3
-
2
-
-
0034691198
-
Measuring the Rate of Intramolecular Contact Formation in Polypeptides
-
L. J. Lapidus, W. A. Eaton, and J. Hofrichter, Measuring the Rate of Intramolecular Contact Formation in Polypeptides, Proc. Natl. Acad. Sci. U.S.A. 97, 7220 (2000).
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 7220
-
-
Lapidus, L.J.1
Eaton, W.A.2
Hofrichter, J.3
-
3
-
-
77957117205
-
Rate Theories for Biologists
-
H.-X. Zhou, Rate Theories for Biologists, Q. Rev. Biophys. 43, 219 (2010).
-
(2010)
Q. Rev. Biophys.
, vol.43
, pp. 219
-
-
Zhou, H.-X.1
-
4
-
-
81055126961
-
Locating the Barrier for Folding of Single Molecules under an External Force
-
O. K. Dudko, T. G.W. Graham, and R. B. Best, Locating the Barrier for Folding of Single Molecules under an External Force, Phys. Rev. Lett. 107, 208301 (2011).
-
(2011)
Phys. Rev. Lett.
, vol.107
, pp. 208301
-
-
Dudko, O.K.1
Graham, T.G.W.2
Best, R.B.3
-
5
-
-
79960622883
-
Compaction and Tensile Forces Determine the Accuracy of Folding Landscape Parameters from Single Molecule Pulling Experiments
-
G. Morrison, C. Hyeon, M. Hinczewski, and D. Thirumalai, Compaction and Tensile Forces Determine the Accuracy of Folding Landscape Parameters from Single Molecule Pulling Experiments. Phys. Rev. Lett. 106, 138102 (2011).
-
(2011)
Phys. Rev. Lett.
, vol.106
, pp. 138102
-
-
Morrison, G.1
Hyeon, C.2
Hinczewski, M.3
Thirumalai, D.4
-
6
-
-
2142746284
-
The Activated Complex in Chemical Reactions
-
H. Eyring, The Activated Complex in Chemical Reactions, J. Chem. Phys. 3, 107 (1935).
-
(1935)
J. Chem. Phys.
, vol.3
, pp. 107
-
-
Eyring, H.1
-
7
-
-
33748374124
-
Statistical Mechanics of Isomerization Dynamics in Liquids and the Transition State Approximation
-
D. Chandler, Statistical Mechanics of Isomerization Dynamics in Liquids and the Transition State Approximation, J. Chem. Phys. 68, 2959 (1978).
-
(1978)
J. Chem. Phys.
, vol.68
, pp. 2959
-
-
Chandler, D.1
-
8
-
-
84893197664
-
-
arXiv:1108.2304
-
J. D. Chodera, P. J. Elms, W. C. Swope, J.-H. Prinz, S. Marqusee, C. Bustamante, F. Noé, and V. S. Pande, A Robust Approach to Estimating Rates from Time-Correlation Functions, arXiv:1108.2304.
-
A Robust Approach to Estimating Rates from Time-Correlation Functions
-
-
Chodera, J.D.1
Elms, P.J.2
Swope, W.C.3
Prinz, J.-H.4
Marqusee, S.5
Bustamante, C.6
Noé, F.7
Pande, V.S.8
-
9
-
-
0016379116
-
Fluorescence Correlation Spectroscopy. I. Conceptual Basis and Theory
-
E. L. Elson, and D. Magde, Fluorescence Correlation Spectroscopy. I. Conceptual Basis and Theory, Biopolymers 13, 1 (1974).
-
(1974)
Biopolymers
, vol.13
, pp. 1
-
-
Elson, E.L.1
Magde, D.2
-
10
-
-
0001540218
-
Relaxation Processes and Chemical Kinetics
-
J. L. Skinner and P. G. Wolynes, Relaxation Processes and Chemical Kinetics, J. Chem. Phys. 69, 2143 (1978).
-
(1978)
J. Chem. Phys.
, vol.69
, pp. 2143
-
-
Skinner, J.L.1
Wolynes, P.G.2
-
11
-
-
34247382025
-
Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations
-
J. D. Chodera, W. C. Swope, J.W. Pitera, and K. A. Dill, Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations, Multiscale Model. Simul. 5, 1214 (2006).
-
(2006)
Multiscale Model. Simul.
, vol.5
, pp. 1214
-
-
Chodera, J.D.1
Swope, W.C.2
Pitera, J.W.3
Dill, K.A.4
-
12
-
-
34247338100
-
Automatic Discovery of Metastable States for the Construction of Markov Models of Macromolecular Conformational Dynamics
-
J. D. Chodera, K. A. Dill, N. Singhal, V. S. Pande, W. C. Swope, and J.W. Pitera, Automatic Discovery of Metastable States for the Construction of Markov Models of Macromolecular Conformational Dynamics, J. Chem. Phys. 126, 155101 (2007).
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 155101
-
-
Chodera, J.D.1
Dill, K.A.2
Singhal, N.3
Pande, V.S.4
Swope, W.C.5
Pitera, J.W.6
-
13
-
-
34247339716
-
Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States
-
F. Noé, I. Horenko, C. Schütte, and J. C. Smith, Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States, J. Chem. Phys. 126, 155102 (2007).
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 155102
-
-
Noé, F.1
Horenko, I.2
Schütte, C.3
Smith, J.C.4
-
14
-
-
79957488000
-
Markov Models of Molecular Kinetics: Generation and Validation
-
J.-H. Prinz, H. Wu, M. Sarich, B. Keller, M. Fischbach, M. Held, J. D. Chodera, C. Schütte, and F. Noé, Markov Models of Molecular Kinetics: Generation and Validation, J. Chem. Phys. 134, 174105 (2011).
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 174105
-
-
Prinz, J.-H.1
Wu, H.2
Sarich, M.3
Keller, B.4
Fischbach, M.5
Held, M.6
Chodera, J.D.7
Schütte, C.8
Noé, F.9
-
15
-
-
2942567954
-
Describing Protein Folding Kinetics by Molecular Dynamics Simulations: 1. Theory
-
W. C. Swope, J.W. Pitera, and F. Suits, Describing Protein Folding Kinetics by Molecular Dynamics Simulations: 1. Theory, J. Phys. Chem. B 108, 6571 (2004).
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 6571
-
-
Swope, W.C.1
Pitera, J.W.2
Suits, F.3
-
16
-
-
77956841151
-
On the Approximation Quality of Markov State Models
-
M. Sarich, F. Noé, and C. Schütte, On the Approximation Quality of Markov State Models, SIAM Multiscale Model. Simul. 8, 1154 (2010).
-
(2010)
SIAM Multiscale Model. Simul.
, vol.8
, pp. 1154
-
-
Sarich, M.1
Noé, F.2
Schütte, C.3
-
17
-
-
33846326884
-
A Coarse-Graining Method for the Identification of Transition Rates between Molecular Conformations
-
S. Kube and M. Weber, A Coarse-Graining Method for the Identification of Transition Rates between Molecular Conformations, J. Chem. Phys. 126, 024103 (2007).
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 024103
-
-
Kube, S.1
Weber, M.2
-
18
-
-
44949178407
-
Coarse Master Equations for Peptide Folding Dynamics
-
N. V. Buchete and G. Hummer, Coarse Master Equations for Peptide Folding Dynamics, J. Phys. Chem. B 112, 6057 (2008).
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 6057
-
-
Buchete, N.V.1
Hummer, G.2
-
19
-
-
79958151345
-
Markov State Models Based on Milestoning
-
C. Schütte, F. Noé, J. Lu, M. Sarich, and E. Vanden-Eijnden, Markov State Models Based on Milestoning, J. Chem. Phys. 134, 204105 (2011).
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 204105
-
-
Schütte, C.1
Noé, F.2
Lu, J.3
Sarich, M.4
Vanden-Eijnden, E.5
-
20
-
-
79958852980
-
Dynamics of Protein Folding: Probing the Kinetic Network of Folding-Unfolding Transitions with Experiment and Theory
-
G. S. Buchner, R. D. Murphy, N.-V. Buchete, and J. Kubelka, Dynamics of Protein Folding: Probing the Kinetic Network of Folding-Unfolding Transitions with Experiment and Theory, Biochim. Biophys. Acta 1814, 1001 (2011).
-
(2011)
Biochim. Biophys. Acta
, vol.1814
, pp. 1001
-
-
Buchner, G.S.1
Murphy, R.D.2
Buchete, N.-V.3
Kubelka, J.4
-
21
-
-
0024610919
-
A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition
-
L. R. Rabiner, A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition, Proc. IEEE 77, 257. 1989).
-
(1989)
Proc. IEEE
, vol.77
, pp. 257
-
-
Rabiner, L.R.1
-
22
-
-
33746747438
-
Analysis of Single-Molecule FRET Trajectories Using Hidden Markov Modeling
-
S. A. McKinney, C. Joo, and T. Ha, Analysis of Single-Molecule FRET Trajectories Using Hidden Markov Modeling, Biophys. J. 91, 1941 (2006).
-
(2006)
Biophys. J.
, vol.91
, pp. 1941
-
-
McKinney, S.A.1
Joo, C.2
Ha, T.3
-
23
-
-
84857992042
-
-
arXiv:1108.1430
-
J. D. Chodera, P. Elms, F. Noé, B. Keller, C.M. Kaiser, A. Ewall-Wice, S. Marqusee, C. Bustamante, and N. S. Hinrichs, Bayesian Hidden Markov Model Analysis of Single-Molecule Force Spectroscopy: Characterizing Kinetics under Measurement Uncertainty, arXiv:1108.1430.
-
Bayesian Hidden Markov Model Analysis of Single-Molecule Force Spectroscopy: Characterizing Kinetics under Measurement Uncertainty
-
-
Chodera, J.D.1
Elms, P.2
Noé, F.3
Keller, B.4
Kaiser, C.M.5
Ewall-Wice, A.6
Marqusee, S.7
Bustamante, C.8
Hinrichs, N.S.9
-
24
-
-
68149166290
-
Decoding the Pattern of Photon Colors in Single-Molecule FRET
-
I. V. Gopich and A. Szabo, Decoding the Pattern of Photon Colors in Single-Molecule FRET, J. Phys. Chem. B 113, 10 965 (2009).
-
(2009)
J. Phys. Chem. B
, vol.113
, Issue.10
, pp. 965
-
-
Gopich, I.V.1
Szabo, A.2
-
25
-
-
80055087629
-
The Complex Folding Network of Single Calmodulin Molecules
-
J. Stigler, F. Ziegler, A. Gieseke, J. C. M. Gebhardt, and M. Rief, The Complex Folding Network of Single Calmodulin Molecules, Science 334, 512 (2011).
-
(2011)
Science
, vol.334
, pp. 512
-
-
Stigler, J.1
Ziegler, F.2
Gieseke, A.3
Gebhardt, J.C.M.4
Rief, M.5
-
26
-
-
80055033153
-
Single-Molecule Fluorescence Spectroscopy Maps the Folding Landscape of a Large Protein
-
M. Pirchi, G. Ziv, I. Riven, S. S. Cohen, N. Zohar, Y. Barak, and G. Haran, Single-Molecule Fluorescence Spectroscopy Maps the Folding Landscape of a Large Protein, Nat. Commun. 2, 493 (2011).
-
(2011)
Nat. Commun.
, vol.2
, pp. 493
-
-
Pirchi, M.1
Ziv, G.2
Riven, I.3
Cohen, S.S.4
Zohar, N.5
Barak, Y.6
Haran, G.7
-
27
-
-
84255177954
-
Signal-Pair Correlation Analysis of Single-Molecule Trajectories
-
A. Hoffmann and M. T. Woodside, Signal-Pair Correlation Analysis of Single-Molecule Trajectories, Angew. Chem., Int. Ed. Engl. 50, 12643 (2011).
-
(2011)
Angew. Chem. Int. Ed. Engl.
, vol.50
, pp. 12643
-
-
Hoffmann, A.1
Woodside, M.T.2
-
28
-
-
84900309765
-
-
See Supplemental Material at for detailed derivations of the theory summarized in this paper, and for additional data on Apomyoglobin.
-
See Supplemental Material at http://link.aps.org/ supplemental/10.1103/PhysRevX.4.011020 for detailed derivations of the theory summarized in this paper, and for additional data on Apomyoglobin.
-
-
-
-
29
-
-
0031100955
-
Detailed Balance in Nonequilibrium Systems
-
F. Barra, M. Clerc, and E. Tirapegui, Detailed Balance in Nonequilibrium Systems, Dyn. Stab. Syst. 12, 61 (1997).
-
(1997)
Dyn. Stab. Syst.
, vol.12
, pp. 61
-
-
Barra, F.1
Clerc, M.2
Tirapegui, E.3
-
30
-
-
0000573002
-
A Direct Approach to Conformational Dynamics Based on Hybrid Monte Carlo
-
C. Schütte, A. Fischer, W. Huisinga, and P. Deuflhard, A Direct Approach to Conformational Dynamics Based on Hybrid Monte Carlo, J. Comput. Phys. 151, 146 (1999).
-
(1999)
J. Comput. Phys.
, vol.151
, pp. 146
-
-
Schütte, C.1
Fischer, A.2
Huisinga, W.3
Deuflhard, P.4
-
31
-
-
84879735744
-
A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems SIAM Multiscale
-
F. Noé and F. Nüske, A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems SIAM Multiscale Model. Simul. 11, 635 (2013).
-
(2013)
Model. Simul.
, vol.11
, pp. 635
-
-
Noé, F.1
Nüske, F.2
-
32
-
-
78650749027
-
Deconvolution of Dynamic Mechanical Networks
-
M. Hinczewski, Y. von Hansen, and R. R. Netz, Deconvolution of Dynamic Mechanical Networks, Proc. Natl. Acad. Sci. U.S.A. 107, 21493 (2010).
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 21493
-
-
Hinczewski, M.1
von Hansen, Y.2
Netz, R.R.3
-
33
-
-
84867021896
-
Auto-and Cross-Power Spectral Analysis of Dual Trap Optical Tweezer Experiments Using Bayesian Inference
-
Y. von Hansen, A. Mehlich, B. Pelz, M. Rief, and R. R. Netz, Auto-and Cross-Power Spectral Analysis of Dual Trap Optical Tweezer Experiments Using Bayesian Inference, Rev. Sci. Instrum. 83, 095116 (2012).
-
(2012)
Rev. Sci. Instrum.
, vol.83
, pp. 095116
-
-
von Hansen, Y.1
Mehlich, A.2
Pelz, B.3
Rief, M.4
Netz, R.R.5
-
34
-
-
84875249565
-
From Mechanical Folding Trajectories to Intrinsic Energy Landscapes of Biopolymers
-
M. Hinczewski, J. C. M. Gebhardt, M. Rief, and D. Thirumalai, From Mechanical Folding Trajectories to Intrinsic Energy Landscapes of Biopolymers, Proc. Natl. Acad. Sci. U.S.A. 110, 4500 (2013).
-
(2013)
Proc. Natl. Acad. Sci. U.S.A.
, vol.110
, pp. 4500
-
-
Hinczewski, M.1
Gebhardt, J.C.M.2
Rief, M.3
Thirumalai, D.4
-
35
-
-
36149006040
-
Reciprocal Relations in Irreversible Processes II
-
L. Onsager, Reciprocal Relations in Irreversible Processes II, Phys. Rev. 38, 2265 (1931).
-
(1931)
Phys. Rev.
, vol.38
, pp. 2265
-
-
Onsager, L.1
-
36
-
-
0001538813
-
Trajectory Analysis of a Kinetic Theory for Isomerization Dynamics in Condensed Phases
-
J. A. Montgomery, D. Chandler, and B. J. Berne, Trajectory Analysis of a Kinetic Theory for Isomerization Dynamics in Condensed Phases, J. Chem. Phys. 70, 4056 (1979).
-
(1979)
J. Chem. Phys.
, vol.70
, pp. 4056
-
-
Montgomery, J.A.1
Chandler, D.2
Berne, B.J.3
-
37
-
-
36049058132
-
Statistical Error Due to Finite Time Averaging in Computer Experiments
-
R. Zwanzig and N. K. Ailawadi, Statistical Error Due to Finite Time Averaging in Computer Experiments, Phys. Rev. 182, 280 (1969).
-
(1969)
Phys. Rev.
, vol.182
, pp. 280
-
-
Zwanzig, R.1
Ailawadi, N.K.2
-
38
-
-
0343262489
-
über Eine Neue Methode zur Lösung Gewisser Variationsprobleme der Mathematischen Physik
-
W. Ritz, über Eine Neue Methode zur Lösung Gewisser Variationsprobleme der Mathematischen Physik, J. Reine Angew. Math. 135, 1 (1909).
-
(1909)
J. Reine Angew. Math.
, vol.135
, pp. 1
-
-
Ritz, W.1
-
39
-
-
33846071499
-
Using the Histogram Test to Quantify Reaction Coordinate Error
-
B. Peters, Using the Histogram Test to Quantify Reaction Coordinate Error, J. Chem. Phys. 125, 241101 (2006).
-
(2006)
J. Chem. Phys.
, vol.125
, pp. 241101
-
-
Peters, B.1
-
40
-
-
70450255797
-
Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations
-
F. Noé, C. Schütte, E. Vanden-Eijnden, L. Reich, and T. R. Weikl, Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations, Proc. Natl. Acad. Sci. U.S.A. 106, 19011 (2009).
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 19011
-
-
Noé, F.1
Schütte, C.2
Vanden-Eijnden, E.3
Reich, L.4
Weikl, T.R.5
-
41
-
-
76149136021
-
Molecular Simulation of Ab Initio Protein Folding for a Millisecond Folder NTL9
-
V. A. Voelz, G. R. Bowman, K. Beauchamp, and V. S. Pande, Molecular Simulation of Ab Initio Protein Folding for a Millisecond Folder NTL9, J. Am. Chem. Soc. 132, 1526 (2010).
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 1526
-
-
Voelz, V.A.1
Bowman, G.R.2
Beauchamp, K.3
Pande, V.S.4
-
42
-
-
70349631761
-
Progress and Challenges in the Automated Construction of Markov State Models for Full Protein Systems
-
G. R. Bowman, K. A. Beauchamp, G. Boxer, and V. S. Pande, Progress and Challenges in the Automated Construction of Markov State Models for Full Protein Systems, J. Chem. Phys. 131, 124101 (2009).
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 124101
-
-
Bowman, G.R.1
Beauchamp, K.A.2
Boxer, G.3
Pande, V.S.4
-
44
-
-
0034370539
-
Identification of Almost-Invariant Aggregates in Reversibly Nearly Uncoupled Markov Chains
-
P. Deuflhard, W. Huisinga, A. Fischer, and C. Schütte, Identification of Almost-Invariant Aggregates in Reversibly Nearly Uncoupled Markov Chains. Linear Algebra Appl. 315, 39 (2000).
-
(2000)
Linear Algebra Appl.
, vol.315
, pp. 39
-
-
Deuflhard, P.1
Huisinga, W.2
Fischer, A.3
Schütte, C.4
-
45
-
-
84867004600
-
Limitations of Constant-Force-Feedback Experiments
-
P. J. Elms, J. D. Chodera, C. Bustamante, and S. Marqusee, Limitations of Constant-Force-Feedback Experiments, Biophys. J. 103, 1490 (2012).
-
(2012)
Biophys. J.
, vol.103
, pp. 1490
-
-
Elms, P.J.1
Chodera, J.D.2
Bustamante, C.3
Marqusee, S.4
-
46
-
-
84857926431
-
The Molten Globule State is Unusually Deformable under Mechanical Force
-
P. J. Elms, J. D. Chodera, C. Bustamante, and S. Marqusee, The Molten Globule State is Unusually Deformable under Mechanical Force, Proc. Natl. Acad. Sci. U.S.A. 109, 3796 (2012).
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 3796
-
-
Elms, P.J.1
Chodera, J.D.2
Bustamante, C.3
Marqusee, S.4
|