-
1
-
-
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 10.1021/jp037421y
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 6571-6581
-
-
Swope, W.C.1
Pitera, J.W.2
Suits, F.3
-
2
-
-
34247339716
-
Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable states
-
Noé, F.; Horenko, I.; Schütte, C.; Smith, J. C. Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable states. J. Chem. Phys. 2007, 126, 155102 10.1063/1.2714539.
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 155102
-
-
Noé, F.1
Horenko, I.2
Schütte, C.3
Smith, J.C.4
-
3
-
-
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 10.1063/1.2714538.
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 155101
-
-
Chodera, J.D.1
Singhal, N.2
Pande, V.S.3
Dill, K.A.4
Swope, W.C.5
-
4
-
-
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 10.1021/jp0761665
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 6057-6069
-
-
Buchete, N.-V.1
Hummer, G.2
-
5
-
-
79957488000
-
Markov models of molecular kinetics: Generation and Validation
-
Prinz, J.-H.; Wu, H.; Sarich, M.; Keller, B. G.; Senne, M.; Held, M.; Chodera, J. D.; Schütte, C.; Noé, F. Markov models of molecular kinetics: Generation and Validation J. Chem. Phys. 2011, 134, 174105 10.1063/1.3565032
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 174105
-
-
Prinz, J.-H.1
Wu, H.2
Sarich, M.3
Keller, B.G.4
Senne, M.5
Held, M.6
Chodera, J.D.7
Schütte, C.8
Noé, F.9
-
6
-
-
84959194726
-
-
Eds. Advances in Experimental Medicine and Biology, Springer: Dordrecht, The Netherlands.
-
Bowman, G. R.; Pande, V. S.; Noé, F., Eds. An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation; Advances in Experimental Medicine and Biology, Vol. 797; Springer: Dordrecht, The Netherlands, 2014.
-
(2014)
An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation
, vol.797
-
-
Bowman, G.R.1
Pande, V.S.2
Noé, F.3
-
7
-
-
19644394100
-
Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps
-
Coifman, R. R.; Lafon, S.; Lee, A. B.; Maggioni, M.; Nadler, B.; Warner, F.; Zucker, S. W. Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 7426-7431 10.1073/pnas.0500334102
-
(2005)
Proc. Natl. Acad. Sci. U. S. A.
, vol.102
, pp. 7426-7431
-
-
Coifman, R.R.1
Lafon, S.2
Lee, A.B.3
Maggioni, M.4
Nadler, B.5
Warner, F.6
Zucker, S.W.7
-
8
-
-
79953320021
-
Determination of reaction coordinates via locally scaled diffusion map
-
Rohrdanz, M. A.; Zheng, W.; Maggioni, M.; Clementi, C. Determination of reaction coordinates via locally scaled diffusion map. J. Chem. Phys. 2011, 134, 124116 10.1063/1.3569857
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 124116
-
-
Rohrdanz, M.A.1
Zheng, W.2
Maggioni, M.3
Clementi, C.4
-
9
-
-
80051959824
-
Simplifying the representation of complex free-energy landscapes using sketch-map
-
Ceriotti, M.; Tribello, G. A.; Parrinello, M. Simplifying the representation of complex free-energy landscapes using sketch-map Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 13023-13028 10.1073/pnas.1108486108
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, pp. 13023-13028
-
-
Ceriotti, M.1
Tribello, G.A.2
Parrinello, M.3
-
10
-
-
46249127902
-
Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis
-
Altis, A.; Otten, M.; Nguyen, P. H.; Hegger, R.; Stock, G. Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis J. Chem. Phys. 2008, 128, 245102 10.1063/1.2945165
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 245102
-
-
Altis, A.1
Otten, M.2
Nguyen, P.H.3
Hegger, R.4
Stock, G.5
-
11
-
-
84862891798
-
Optimizing transition states via kernel-based machine learning
-
Pozun, Z. D.; Hansen, K.; Sheppard, D.; Rupp, M.; Muller, K.-R.; Henkelman, G. Optimizing transition states via kernel-based machine learning J. Chem. Phys. 2012, 136, 174101-1-174101-9 10.1063/1.4707167
-
(2012)
J. Chem. Phys.
, vol.136
, pp. 1741011-1741019
-
-
Pozun, Z.D.1
Hansen, K.2
Sheppard, D.3
Rupp, M.4
Muller, K.-R.5
Henkelman, G.6
-
12
-
-
79952585022
-
Toward identification of the reaction coordinate directly from the transition state ensemble using the kernel PCA method
-
Antoniou, D.; Schwartz, S. D. Toward identification of the reaction coordinate directly from the transition state ensemble using the kernel PCA method J. Phys. Chem. B 2011, 115, 2465-2469 10.1021/jp111682x
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 2465-2469
-
-
Antoniou, D.1
Schwartz, S.D.2
-
13
-
-
34547354279
-
Extensions to the likelihood maximization approach for finding reaction coordinates
-
Peters, B.; Beckham, G. T.; Trout, B. L. Extensions to the likelihood maximization approach for finding reaction coordinates J. Chem. Phys. 2007, 127, 034109 10.1063/1.2748396
-
(2007)
J. Chem. Phys.
, vol.127
, pp. 034109
-
-
Peters, B.1
Beckham, G.T.2
Trout, B.L.3
-
14
-
-
84875991078
-
Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions
-
Rohrdanz, M. A.; Zheng, W.; Clementi, C. Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions Annu. Rev. Phys. Chem. 2013, 64, 295-316 10.1146/annurev-physchem-040412-110006
-
(2013)
Annu. Rev. Phys. Chem.
, vol.64
, pp. 295-316
-
-
Rohrdanz, M.A.1
Zheng, W.2
Clementi, C.3
-
15
-
-
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 10.1006/jcph.1999.6231
-
(1999)
J. Comput. Phys.
, vol.151
, pp. 146-168
-
-
Schütte, C.1
Fischer, A.2
Huisinga, W.3
Deuflhard, P.4
-
16
-
-
77956841151
-
On the approximation quality of Markov state models
-
Sarich, M.; Noé, F.; Schütte, C. On the approximation quality of Markov state models Multiscale Model. Simul. 2010, 8, 1154-1177 10.1137/090764049
-
(2010)
Multiscale Model. Simul.
, vol.8
, pp. 1154-1177
-
-
Sarich, M.1
Noé, F.2
Schütte, C.3
-
17
-
-
84879735744
-
A variational approach to modeling slow processes in stochastic dynamical systems
-
Noé, F.; Nüske, F. A variational approach to modeling slow processes in stochastic dynamical systems Multiscale Model. Simul. 2013, 11, 635-655 10.1137/110858616
-
(2013)
Multiscale Model. Simul.
, vol.11
, pp. 635-655
-
-
Noé, F.1
Nüske, F.2
-
18
-
-
84900320724
-
Spectral rate theory for two-state kinetics
-
Prinz, J.-H.; Chodera, J. D.; Noé, F. Spectral rate theory for two-state kinetics Phys. Rev. X 2014, 4, 011020 10.1103/PhysRevX.4.011020
-
(2014)
Phys. Rev. X
, vol.4
, pp. 011020
-
-
Prinz, J.-H.1
Chodera, J.D.2
Noé, F.3
-
19
-
-
84898431921
-
Variational Approach to Molecular Kinetics
-
Nüske, F.; Keller, B. G.; Pérez-Hernández, G.; Mey, A. S. J. S.; Noé, F. Variational Approach to Molecular Kinetics J. Chem. Theory Comput. 2014, 10, 1739-1752 10.1021/ct4009156
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 1739-1752
-
-
Nüske, F.1
Keller, B.G.2
Pérez-Hernández, G.3
Mey, A.S.J.S.4
Noé, F.5
-
20
-
-
84923869832
-
Gaussian Markov transition models of molecular kinetics
-
Wu, H.; Noé, F. Gaussian Markov transition models of molecular kinetics J. Chem. Phys. 2015, 142, 084104 10.1063/1.4913214
-
(2015)
J. Chem. Phys.
, vol.142
, pp. 084104
-
-
Wu, H.1
Noé, F.2
-
21
-
-
84886081379
-
Identification of slow molecular order parameters for Markov model construction
-
Perez-Hernandez, G.; Paul, F.; Giorgino, T.; de Fabritiis, G.; Noé, F. Identification of slow molecular order parameters for Markov model construction J. Chem. Phys. 2013, 139, 015102 10.1063/1.4811489
-
(2013)
J. Chem. Phys.
, vol.139
, pp. 015102
-
-
Perez-Hernandez, G.1
Paul, F.2
Giorgino, T.3
De Fabritiis, G.4
Noé, F.5
-
22
-
-
84876005630
-
Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
-
Schwantes, C. R.; Pande, V. S. Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9 J. Chem. Theory Comput. 2013, 9, 2000-2009 10.1021/ct300878a
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 2000-2009
-
-
Schwantes, C.R.1
Pande, V.S.2
-
23
-
-
84922674715
-
Modeling Molecular Kinetics with tICA and the Kernel Trick
-
Schwantes, C. R.; Pande, V. S. Modeling Molecular Kinetics with tICA and the Kernel Trick J. Chem. Theory Comput. 2015, 11, 600-608 10.1021/ct5007357
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 600-608
-
-
Schwantes, C.R.1
Pande, V.S.2
-
24
-
-
79959761281
-
Which Similarity Measure Is Better for Analyzing Protein Structures in a Molecular Dynamics Trajectory?
-
Cossio, P.; Laio, A.; Pietrucci, F. Which Similarity Measure Is Better for Analyzing Protein Structures in a Molecular Dynamics Trajectory? Phys. Chem. Chem. Phys. 2011, 13, 10421-10425 10.1039/c0cp02675a
-
(2011)
Phys. Chem. Chem. Phys.
, vol.13
, pp. 10421-10425
-
-
Cossio, P.1
Laio, A.2
Pietrucci, F.3
-
25
-
-
84880033049
-
Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics
-
McGibbon, R. T.; Pande, V. S. Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics J. Chem. Theory Comput. 2013, 9, 2900-2906 10.1021/ct400132h
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 2900-2906
-
-
McGibbon, R.T.1
Pande, V.S.2
-
26
-
-
84865064420
-
Distribution of Reciprocal of Interatomic Distances: A Fast Structural Metric
-
Zhou, T.; Caflisch, A. Distribution of Reciprocal of Interatomic Distances: A Fast Structural Metric J. Chem. Theory Comput. 2012, 8, 2930-2937 10.1021/ct3003145
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 2930-2937
-
-
Zhou, T.1
Caflisch, A.2
-
27
-
-
84864071145
-
Diffusion Maps, Spectral Clustering and Eigenfunctions of Fokker-Planck Operators
-
Nadler, B.; Lafon, S.; Kevrekidis, I. G.; Coifman, R. R. Diffusion Maps, Spectral Clustering and Eigenfunctions of Fokker-Planck Operators Adv. Neural Inf. Process. Syst. 2005, 18, 955-962
-
(2005)
Adv. Neural Inf. Process. Syst.
, vol.18
, pp. 955-962
-
-
Nadler, B.1
Lafon, S.2
Kevrekidis, I.G.3
Coifman, R.R.4
-
28
-
-
84906569206
-
Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics
-
Preto, J.; Clementi, C. Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics Phys. Chem. Chem. Phys. 2014, 16, 19181-19191 10.1039/C3CP54520B
-
(2014)
Phys. Chem. Chem. Phys.
, vol.16
, pp. 19181-19191
-
-
Preto, J.1
Clementi, C.2
-
29
-
-
84863672816
-
EMMA-A software package for Markov model building and analysis
-
Senne, M.; Trendelkamp-Schroer, B.; Mey, A. S. J. S.; Schütte, C.; Noé, F. EMMA-A software package for Markov model building and analysis J. Chem. Theory Comput. 2012, 8, 2223-2238 10.1021/ct300274u
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 2223-2238
-
-
Senne, M.1
Trendelkamp-Schroer, B.2
Mey, A.S.J.S.3
Schütte, C.4
Noé, F.5
-
30
-
-
80053979296
-
MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale
-
Beauchamp, K. A.; Bowman, G. R.; Lane, T. J.; Maibaum, L.; Haque, I. S.; Pande, V. S. MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale J. Chem. Theory Comput. 2011, 7, 3412-3419 10.1021/ct200463m
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 3412-3419
-
-
Beauchamp, K.A.1
Bowman, G.R.2
Lane, T.J.3
Maibaum, L.4
Haque, I.S.5
Pande, V.S.6
-
31
-
-
58149421595
-
Analysis of a complex of statistical variables into principal components
-
Hotelling, H. Analysis of a complex of statistical variables into principal components J. Edu. Psych. 1933, 24, 417-441 10.1037/h0071325
-
(1933)
J. Edu. Psych.
, vol.24
, pp. 417-441
-
-
Hotelling, H.1
-
32
-
-
0027441950
-
Essential dynamics of proteins
-
Amadei, A.; Linssen, A. B.; Berendsen, H. J. C. Essential dynamics of proteins Proteins: Struct., Funct., Genet. 1993, 17, 412-225 10.1002/prot.340170408
-
(1993)
Proteins: Struct., Funct., Genet.
, vol.17
, pp. 412-225
-
-
Amadei, A.1
Linssen, A.B.2
Berendsen, H.J.C.3
-
33
-
-
84944103364
-
Pseudo generators of spatial transfer operators
-
Bittracher, A.; Koltai, P.; Junge, O. Pseudo generators of spatial transfer operators. 2014, arXiv:1412.1733 (http://arxiv.org/abs/1412.1733).
-
(2014)
arXiv:1412.1733
-
-
Bittracher, A.1
Koltai, P.2
Junge, O.3
-
34
-
-
84944103365
-
Estimation and uncertainty of reversible Markov models
-
Submitted to, (preprint available at arXiv:1507.05990).
-
Trendelkamp-Schroer, B.; Wu, H.; Paul, F.; Noé, F. Estimation and uncertainty of reversible Markov models. Submitted to J. Chem. Phys., 2015, (preprint available at arXiv:1507.05990, http://arxiv.org/abs/1507.05990).
-
(2015)
J. Chem. Phys.
-
-
Trendelkamp-Schroer, B.1
Wu, H.2
Paul, F.3
Noé, F.4
-
35
-
-
0024610919
-
A tutorial on hidden Markov models and selected applications in speech recognition
-
Rabiner, L. A tutorial on hidden Markov models and selected applications in speech recognition Proc. IEEE 1989, 77, 257-286 10.1109/5.18626
-
(1989)
Proc. IEEE
, vol.77
, pp. 257-286
-
-
Rabiner, L.1
-
36
-
-
77957937199
-
Atomic-Level Characterization of the Structural Dynamics of Proteins
-
Shaw, D. E.; Maragakis, P.; Lindorff-Larsen, K.; Piana, S.; Dror, R.; Eastwood, M.; Bank, J.; Jumper, J.; Salmon, J.; Shan, Y.; Wriggers, W. Atomic-Level Characterization of the Structural Dynamics of Proteins Science 2010, 330, 341-346 10.1126/science.1187409
-
(2010)
Science
, vol.330
, pp. 341-346
-
-
Shaw, D.E.1
Maragakis, P.2
Lindorff-Larsen, K.3
Piana, S.4
Dror, R.5
Eastwood, M.6
Bank, J.7
Jumper, J.8
Salmon, J.9
Shan, Y.10
Wriggers, W.11
-
37
-
-
84903361996
-
Projected and Hidden Markov Models for calculating kinetics and metastable states of complex molecules
-
Noé, F.; Wu, H.; Prinz, J.-H.; Plattner, N. Projected and Hidden Markov Models for calculating kinetics and metastable states of complex molecules J. Chem. Phys. 2013, 139, 184114 10.1063/1.4828816
-
(2013)
J. Chem. Phys.
, vol.139
, pp. 184114
-
-
Noé, F.1
Wu, H.2
Prinz, J.-H.3
Plattner, N.4
-
38
-
-
79960007037
-
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
-
Buch, I.; Giorgino, T.; de Fabritiis, G. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 10184-10189 10.1073/pnas.1103547108
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, pp. 10184-10189
-
-
Buch, I.1
Giorgino, T.2
De Fabritiis, G.3
-
39
-
-
84986563426
-
Protein conformational plasticity and complex ligand binding kinetics explored by atomistic simulations and Markov models
-
Plattner, N.; Noé, F. Protein conformational plasticity and complex ligand binding kinetics explored by atomistic simulations and Markov models Nat. Commun. 2015, 6, 7653 10.1038/ncomms8653
-
(2015)
Nat. Commun.
, vol.6
, pp. 7653
-
-
Plattner, N.1
Noé, F.2
-
40
-
-
84922224593
-
Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps
-
Tiwary, P.; Limongelli, V.; Salvalaglio, M.; Parrinello, M. Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps Proc. Natl. Acad. Sci. U. S. A. 2015, 112, E386-E391 10.1073/pnas.1424461112
-
(2015)
Proc. Natl. Acad. Sci. U. S. A.
, vol.112
, pp. E386-E391
-
-
Tiwary, P.1
Limongelli, V.2
Salvalaglio, M.3
Parrinello, M.4
|