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Volumn 11, Issue 10, 2015, Pages 5002-5011

Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation

Author keywords

[No Author keywords available]

Indexed keywords

BENZAMIDINE; BENZAMIDINE DERIVATIVE; TRYPSIN; TRYPSIN INHIBITOR;

EID: 84944046499     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/acs.jctc.5b00553     Document Type: Article
Times cited : (213)

References (40)
  • 1
    • 2942567954 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 7
    • 19644394100 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 12
    • 79952585022 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 20
    • 84923869832 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 28
    • 84906569206 scopus 로고    scopus 로고
    • 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
  • 31
    • 58149421595 scopus 로고
    • 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
  • 33
    • 84944103364 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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
  • 37
    • 84903361996 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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


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