-
1
-
-
0000573002
-
A Direct Approach to Conformational Dynamics Based on Hybrid Monte Carlo
-
Schütte, C.; Fischer, A.; Huisinga, W.; Deuflhard, P. A Direct Approach to Conformational Dynamics Based on Hybrid Monte Carlo J. Comput. Phys. 1999, 151, 146-168
-
(1999)
J. Comput. Phys.
, vol.151
, pp. 146-168
-
-
Schütte, C.1
Fischer, A.2
Huisinga, W.3
Deuflhard, P.4
-
2
-
-
2942567954
-
Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory
-
Swope, W. C.; Pitera, J. W.; Suits, F. Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory J. Phys. Chem. B 2004, 108, 6571-6581
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 6571-6581
-
-
Swope, W.C.1
Pitera, J.W.2
Suits, F.3
-
3
-
-
10944260594
-
Long-Time Conformational Transitions of Alanine Dipeptide in Aqueous Solution: Continuous and Discrete-State Kinetic Models
-
Chekmarev, D. S.; Ishida, T.; Levy, R. M. Long-Time Conformational Transitions of Alanine Dipeptide in Aqueous Solution: Continuous and Discrete-State Kinetic Models J. Phys. Chem. B 2004, 108, 19487-19495
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 19487-19495
-
-
Chekmarev, D.S.1
Ishida, T.2
Levy, R.M.3
-
4
-
-
0035946983
-
Essential Dynamics of Reversible Peptide Folding: Memory-Free Conformational Dynamics Governed by Internal Hydrogen Bonds
-
de Groot, B. L.; Daura, X.; Mark, A. E.; Grubmüller, H. Essential Dynamics of Reversible Peptide Folding: Memory-Free Conformational Dynamics Governed by Internal Hydrogen Bonds J. Mol. Biol. 2001, 309, 299-313
-
(2001)
J. Mol. Biol.
, vol.309
, pp. 299-313
-
-
De Groot, B.L.1
Daura, X.2
Mark, A.E.3
Grubmüller, H.4
-
5
-
-
0000370391
-
The Topology of Multidimensional Potential Energy Surfaces. Theory and Application to Peptide Structure and Kinetics
-
Becker, O. M.; Karplus, M. The Topology of Multidimensional Potential Energy Surfaces. Theory and Application to Peptide Structure and Kinetics J. Chem. Phys. 1997, 106, 1495-1517
-
(1997)
J. Chem. Phys.
, vol.106
, pp. 1495-1517
-
-
Becker, O.M.1
Karplus, M.2
-
6
-
-
17444389688
-
Coarse Master Equation from Bayesian Analysis of Replica Molecular Dynamics Simulations
-
Sriraman, S.; Kevrekidis, L. G.; Hummer, G. Coarse Master Equation from Bayesian Analysis of Replica Molecular Dynamics Simulations J. Phys. Chem. B 2005, 109, 6479-6484
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 6479-6484
-
-
Sriraman, S.1
Kevrekidis, L.G.2
Hummer, G.3
-
7
-
-
70450255797
-
Constructing the Equilibrium Ensemble of Folding Pathways from Short Off-Equilibrium Simulations
-
Noé, F.; Schütte, C.; Vanden-Eijnden, E.; Reich, L.; Weikl, T. R. Constructing the Equilibrium Ensemble of Folding Pathways from Short Off-Equilibrium Simulations Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 19011-19016
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 19011-19016
-
-
Noé, F.1
Schütte, C.2
Vanden-Eijnden, E.3
Reich, L.4
Weikl, T.R.5
-
8
-
-
84864495493
-
Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment
-
Voelz, V. A.; Jager, M.; Yao, S. H.; Chen, Y. J.; Zhu, L.; Waldauer, S. A.; Bowman, G. R.; Friedrichs, M.; Bakajin, O.; Lapidus, L. J. et al. Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment J. Am. Chem. Soc. 2012, 134, 12565-12577
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 12565-12577
-
-
Voelz, V.A.1
Jager, M.2
Yao, S.H.3
Chen, Y.J.4
Zhu, L.5
Waldauer, S.A.6
Bowman, G.R.7
Friedrichs, M.8
Bakajin, O.9
Lapidus, L.J.10
-
9
-
-
0036424048
-
Transition Path Sampling. Throwing Ropes over Rough Mountain Passes in the Dark
-
Bolhuis, P. G.; Chandler, D.; Dellago, C.; Geissler, P. L. Transition Path Sampling. Throwing Ropes Over Rough Mountain Passes in the Dark Annu. Rev. Phys. Chem. 2002, 53, 291-318
-
(2002)
Annu. Rev. Phys. Chem.
, vol.53
, pp. 291-318
-
-
Bolhuis, P.G.1
Chandler, D.2
Dellago, C.3
Geissler, P.L.4
-
10
-
-
0000689085
-
Predicting Slow Structural Transitions in Macromolecular Systems. Conformational Flooding
-
Grubmüller, H. Predicting Slow Structural Transitions in Macromolecular Systems. Conformational Flooding Phys. Rev. E 1995, 52, 2893-2906
-
(1995)
Phys. Rev. E
, vol.52
, pp. 2893-2906
-
-
Grubmüller, H.1
-
11
-
-
0000309559
-
SWARM-MD: Searching Conformational Space by Cooperative Molecular Dynamics
-
Huber, T.; van Gunsteren, W. F. SWARM-MD: Searching Conformational Space by Cooperative Molecular Dynamics J. Phys. Chem. A 1998, 102, 5937-5943
-
(1998)
J. Phys. Chem. A
, vol.102
, pp. 5937-5943
-
-
Huber, T.1
Van Gunsteren, W.F.2
-
12
-
-
0001208056
-
Parallel Replica Method for Dynamics of Infrequent Events
-
Voter, A. F. Parallel Replica Method for Dynamics of Infrequent Events Phys. Rev. B 1998, 57, R13985-R13988
-
(1998)
Phys. Rev. B
, vol.57
, pp. 13985-R13988
-
-
Voter, A.F.1
-
13
-
-
0037067120
-
Peptide Loop-Closure Kinetics from Microsecond Molecular Dynamics Simulations in Explicit Solvent
-
Yeh, I. C.; Hummer, G. Peptide Loop-Closure Kinetics from Microsecond Molecular Dynamics Simulations in Explicit Solvent J. Am. Chem. Soc. 2002, 124, 6563-6568
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 6563-6568
-
-
Yeh, I.C.1
Hummer, G.2
-
14
-
-
0037038372
-
Absolute Comparison of Simulated and Experimental Protein Folding Dynamics
-
Snow, C. D.; Nguyen, N.; Pande, V. S.; Gruebele, M. Absolute Comparison of Simulated and Experimental Protein Folding Dynamics Nature 2002, 420, 102-106
-
(2002)
Nature
, vol.420
, pp. 102-106
-
-
Snow, C.D.1
Nguyen, N.2
Pande, V.S.3
Gruebele, M.4
-
15
-
-
0037865691
-
Coarse Molecular Dynamics of a Peptide Fragment: Free Energy, Kinetics, and Long-Time Dynamics Computations
-
Hummer, G.; Kevrekidis, I. G. Coarse Molecular Dynamics of a Peptide Fragment: Free Energy, Kinetics, and Long-Time Dynamics Computations J. Chem. Phys. 2003, 118, 10762-10773
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 10762-10773
-
-
Hummer, G.1
Kevrekidis, I.G.2
-
16
-
-
55949099868
-
On the Assumptions Underlying Milestoning
-
Vanden-Eijnden, E.; Venturoli, M.; Ciccotti, G.; Elber, R. On the Assumptions Underlying Milestoning J. Chem. Phys. 2008, 129, 174102
-
(2008)
J. Chem. Phys.
, vol.129
-
-
Vanden-Eijnden, E.1
Venturoli, M.2
Ciccotti, G.3
Elber, R.4
-
17
-
-
45949108535
-
Finding Transition Pathways Using the String Method with Swarms of Trajectories
-
Pan, A. C.; Sezer, D.; Roux, B. Finding Transition Pathways Using the String Method with Swarms of Trajectories J. Phys. Chem. B 2008, 112, 3432-3440
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 3432-3440
-
-
Pan, A.C.1
Sezer, D.2
Roux, B.3
-
18
-
-
44949178407
-
Coarse Master Equations for Peptide Folding Dynamics
-
Buchete, N. V.; Hummer, G. Coarse Master Equations for Peptide Folding Dynamics J. Phys. Chem. B 2008, 112, 6057-6069
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 6057-6069
-
-
Buchete, N.V.1
Hummer, G.2
-
19
-
-
84898431921
-
Variational Approach to Molecular Kinetics
-
Nuske, F.; Keller, B. G.; Pérez-Hernández, G.; Mey, A. S. J. S.; Noé, F. Variational Approach to Molecular Kinetics J. Chem. Theory Comp. 2014, 10, 1739-1752
-
(2014)
J. Chem. Theory Comp.
, vol.10
, pp. 1739-1752
-
-
Nuske, F.1
Keller, B.G.2
Pérez-Hernández, G.3
Mey, A.S.J.S.4
Noé, F.5
-
20
-
-
0001630543
-
From Classical Dynamics to Continuous-Time Random Walks
-
Zwanzig, R. From Classical Dynamics to Continuous-Time Random Walks J. Stat. Phys. 1983, 30, 255-262
-
(1983)
J. Stat. Phys.
, vol.30
, pp. 255-262
-
-
Zwanzig, R.1
-
21
-
-
0003474751
-
-
Cambridge University Press: New York, Chapter 2.7.
-
Press, W. H.; Teukolsky, S. A.; Vetterling, W. T.; Flannery, B. P. Numerical Recipes. The Art of Scientific Computing, 3 rd ed.; Cambridge University Press: New York, 2007; Chapter 2.7.
-
(2007)
Numerical Recipes. The Art of Scientific Computing, 3rd Ed.
-
-
Press, W.H.1
Teukolsky, S.A.2
Vetterling, W.T.3
Flannery, B.P.4
-
23
-
-
34247338100
-
Automatic Discovery of Metastable States for the Construction of Markov Models of Macromolecular Conformational Dynamics
-
Chodera, J. D.; Singhal, N.; Pande, V. S.; Dill, K. A.; Swope, W. C. Automatic Discovery of Metastable States for the Construction of Markov Models of Macromolecular Conformational Dynamics J. Chem. Phys. 2007, 126, 155101
-
(2007)
J. Chem. Phys.
, vol.126
-
-
Chodera, J.D.1
Singhal, N.2
Pande, V.S.3
Dill, K.A.4
Swope, W.C.5
-
24
-
-
33846326884
-
A Coarse Graining Method for the Identification of Transition Rates between Molecular Conformations
-
Kube, S.; Weber, M. A Coarse Graining Method for the Identification of Transition Rates Between Molecular Conformations J. Chem. Phys. 2007, 126, 024103
-
(2007)
J. Chem. Phys.
, vol.126
-
-
Kube, S.1
Weber, M.2
-
25
-
-
44349162212
-
A Minimum-Reaction-Flux Solution to Master-Equation Models of Protein Folding
-
Zhou, H. X. A Minimum-Reaction-Flux Solution to Master-Equation Models of Protein Folding J. Chem. Phys. 2008, 128, 195104
-
(2008)
J. Chem. Phys.
, vol.128
-
-
Zhou, H.X.1
-
26
-
-
77958103362
-
A Bayesian Method for Construction of Markov Models to Describe Dynamics on Various Time-Scales
-
Rains, E. K.; Andersen, H. C. A Bayesian Method for Construction of Markov Models to Describe Dynamics on Various Time-Scales J. Chem. Phys. 2010, 133, 144113
-
(2010)
J. Chem. Phys.
, vol.133
-
-
Rains, E.K.1
Andersen, H.C.2
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