메뉴 건너뛰기




Volumn 139, Issue 18, 2013, Pages

Projected and hidden Markov models for calculating kinetics and metastable states of complex molecules

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULAR SYSTEM; BOVINE PANCREATIC TRYPSIN INHIBITORS; HIDDEN MARKOV MODELS (HMMS); MARKOV STATE MODELS; META-STABLE STATE; MOLECULAR DYNAMICS SIMULATIONS; REPRODUCIBILITIES; ROBUST ESTIMATION METHOD;

EID: 84903361996     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4828816     Document Type: Article
Times cited : (146)

References (44)
  • 1
    • 84868122477 scopus 로고    scopus 로고
    • Simple few-state models reveal hidden complexity in protein folding
    • 10.1073/pnas.1201810109
    • K. A. Beauchamp, R. McGibbon, Y.-S. Lin, and V. S. Pande, " Simple few-state models reveal hidden complexity in protein folding.," Proc. Natl. Acad. Sci. U.S.A. 109, 17807-17813 (2012). 10.1073/pnas.1201810109
    • (2012) Proc. Natl. Acad. Sci. U.S.A. , vol.109 , pp. 17807-17813
    • Beauchamp, K.A.1    McGibbon, R.2    Lin, Y.-S.3    Pande, V.S.4
  • 2
    • 84870182404 scopus 로고    scopus 로고
    • Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty
    • 10.1063/1.4755751
    • G. R. Bowman, " Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty.," J. Chem. Phys. 137, 134111 (2012). 10.1063/1.4755751
    • (2012) J. Chem. Phys. , vol.137 , pp. 134111
    • Bowman, G.R.1
  • 3
    • 77950159292 scopus 로고    scopus 로고
    • Enhanced modeling via network theory: Adaptive sampling of Markov state models
    • 10.1021/ct900620b
    • G. R. Bowman, D. L. Ensign, and V. S. Pande, " Enhanced modeling via network theory: Adaptive sampling of Markov state models.," J. Chem. Theory Comput. 6 (3), 787-794 (2010). 10.1021/ct900620b
    • (2010) J. Chem. Theory Comput. , vol.6 , Issue.3 , pp. 787-794
    • Bowman, G.R.1    Ensign, D.L.2    Pande, V.S.3
  • 4
    • 84863939894 scopus 로고    scopus 로고
    • Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites
    • 10.1073/pnas.1209309109
    • G. R. Bowman and P. L. Geissler, " Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites.," Proc. Natl. Acad. Sci. U.S.A. 109, 11681-11686 (2012). 10.1073/pnas.1209309109
    • (2012) Proc. Natl. Acad. Sci. U.S.A. , vol.109 , pp. 11681-11686
    • Bowman, G.R.1    Geissler, P.L.2
  • 5
    • 44949178407 scopus 로고    scopus 로고
    • Coarse master equations for peptide folding dynamics
    • 10.1021/jp0761665
    • N. V. Buchete and G. Hummer, " Coarse master equations for peptide folding dynamics.," J. Phys. Chem. B 112, 6057-6069 (2008). 10.1021/jp0761665
    • (2008) J. Phys. Chem. B , vol.112 , pp. 6057-6069
    • Buchete, N.V.1    Hummer, G.2
  • 6
    • 34247338100 scopus 로고    scopus 로고
    • Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
    • 10.1063/1.2714538
    • 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). 10.1063/1.2714538
    • (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
  • 8
    • 13544256263 scopus 로고    scopus 로고
    • Robust Perron cluster analysis in conformation dynamics
    • edited by M. Dellnitz, S. Kirkland, M. Neumann, and C. Schütte (Elsevier, New York), Vol.
    • P. Deuflhard and M. Weber, " Robust Perron cluster analysis in conformation dynamics.," in Linear Algebra Applications, edited by, M. Dellnitz, S. Kirkland, M. Neumann, and, C. Schütte, (Elsevier, New York, 2005), Vol. 398C, pp. 161-184.
    • (2005) Linear Algebra Applications , vol.398 , pp. 161-184
    • Deuflhard, P.1    Weber, M.2
  • 9
    • 0034370539 scopus 로고    scopus 로고
    • Identification of almost invariant aggregates in reversibly nearly uncoupled Markov chains
    • 10.1016/S0024-3795(00)00095-1
    • P. Deulfhard, W. Huisinga, A. Fischer, and C. Schütte, " Identification of almost invariant aggregates in reversibly nearly uncoupled Markov chains.," Linear Algebr. Appl. 315, 39-59 (2000). 10.1016/S0024-3795(00)00095-1
    • (2000) Linear Algebr. Appl. , vol.315 , pp. 39-59
    • Deulfhard, P.1    Huisinga, W.2    Fischer, A.3    Schütte, C.4
  • 10
    • 84861488757 scopus 로고    scopus 로고
    • Estimating the eigenvalue error of Markov State Models
    • 10.1137/100798910
    • N. Djurdjevac, M. Sarich, and C. Schütte, " Estimating the eigenvalue error of Markov State Models.," Multiscale Model. Simul. 10, 61-81 (2012). 10.1137/100798910
    • (2012) Multiscale Model. Simul. , vol.10 , pp. 61-81
    • Djurdjevac, N.1    Sarich, M.2    Schütte, C.3
  • 12
    • 84867004600 scopus 로고    scopus 로고
    • The limitations of constant-force-feedback experiments
    • 10.1016/j.bpj.2012.06.051
    • P. J. Elms, J. D. Chodera, C. Bustamante, and S. Marqusee, " The limitations of constant-force-feedback experiments.," Biophys. J. 103, 1490 (2012). 10.1016/j.bpj.2012.06.051
    • (2012) Biophys. J. , vol.103 , pp. 1490
    • Elms, P.J.1    Chodera, J.D.2    Bustamante, C.3    Marqusee, S.4
  • 14
    • 76649093956 scopus 로고    scopus 로고
    • Full distance-resolved folding energy landscape of one single protein molecule
    • 10.1073/pnas.0909854107
    • J. C. Gebhardt, T. Bornschlögl, and M. Rief, " Full distance-resolved folding energy landscape of one single protein molecule.," Proc. Natl. Acad. Sci. U.S.A. 107 (5), 2013-2018 (2010). 10.1073/pnas.0909854107
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , Issue.5 , pp. 2013-2018
    • Gebhardt, J.C.1    Bornschlögl, T.2    Rief, M.3
  • 15
    • 34547341247 scopus 로고    scopus 로고
    • Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics
    • 10.1063/1.2740261
    • N. S. Hinrichs and V. S. Pande, " Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics.," J. Chem. Phys. 126, 244101 (2007). 10.1063/1.2740261
    • (2007) J. Chem. Phys. , vol.126 , pp. 244101
    • Hinrichs, N.S.1    Pande, V.S.2
  • 16
    • 84859527217 scopus 로고    scopus 로고
    • Markov models and dynamical fingerprints: Unraveling the complexity of molecular kinetics
    • 10.1016/j.chemphys.2011.08.021
    • B. Keller, J.-H. Prinz, and F. Noé, " Markov models and dynamical fingerprints: Unraveling the complexity of molecular kinetics.," Chem. Phys. 396, 92-107 (2012). 10.1016/j.chemphys.2011.08.021
    • (2012) Chem. Phys. , vol.396 , pp. 92-107
    • Keller, B.1    Prinz, J.-H.2    Noé, F.3
  • 17
    • 33846326884 scopus 로고    scopus 로고
    • A coarse graining method for the identification of transition rates between molecular conformations
    • 10.1063/1.2404953
    • S. Kube and M. Weber, " A coarse graining method for the identification of transition rates between molecular conformations.," J. Chem. Phys. 126 (2), 024103 (2007). 10.1063/1.2404953
    • (2007) J. Chem. Phys. , vol.126 , Issue.2 , pp. 024103
    • Kube, S.1    Weber, M.2
  • 18
    • 0000353178 scopus 로고
    • A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains
    • 10.1214/aoms/1177697196
    • G. Soules, L. E. Baum, T. Petrie, and N. Weiss, " A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains.," Ann. Math. Stat. 41, 164-171 (1970). 10.1214/aoms/ 1177697196
    • (1970) Ann. Math. Stat. , vol.41 , pp. 164-171
    • Soules, G.1    Baum, L.E.2    Petrie, T.3    Weiss, N.4
  • 19
    • 84887578598 scopus 로고    scopus 로고
    • Dynamic neutron scattering from conformational dynamics I: Theory and Markov models
    • 10.1063/1.4824070
    • B. Lindner, Z. Yi, J.-H. Prinz, J. C. Smith, and F. Noé, " Dynamic neutron scattering from conformational dynamics I: Theory and Markov models.," J. Chem. Phys. 139, 175101 (2013). 10.1063/1.4824070
    • (2013) J. Chem. Phys. , vol.139 , pp. 175101
    • Lindner, B.1    Yi, Z.2    Prinz, J.-H.3    Smith, J.C.4    Noé, F.5
  • 20
    • 80055081145 scopus 로고    scopus 로고
    • How fast-folding proteins fold
    • 10.1126/science.1208351
    • K. Lindorff-Larsen, S. Piana, R. O. Dror, and D. E. Shaw, " How fast-folding proteins fold.," Science 334, 517-520 (2011). 10.1126/science.1208351
    • (2011) Science , vol.334 , pp. 517-520
    • Lindorff-Larsen, K.1    Piana, S.2    Dror, R.O.3    Shaw, D.E.4
  • 21
    • 33748366393 scopus 로고    scopus 로고
    • Illustration of transition path theory on a collection of simple examples
    • 10.1063/1.2335447
    • P. Metzner, C. Schütte, and E. Vanden-Eijnden, " Illustration of transition path theory on a collection of simple examples.," J. Chem. Phys. 125 (8), 084110 (2006). 10.1063/1.2335447
    • (2006) J. Chem. Phys. , vol.125 , Issue.8 , pp. 084110
    • Metzner, P.1    Schütte, C.2    Vanden-Eijnden, E.3
  • 22
    • 0000302959 scopus 로고
    • Separation of a mixture of independent signals using time delayed correlations
    • 10.1103/PhysRevLett.72.3634
    • L. Molgedey and H. G. Schuster, " Separation of a mixture of independent signals using time delayed correlations.," Phys. Rev. Lett. 72, 3634-3637 (1994). 10.1103/PhysRevLett.72.3634
    • (1994) Phys. Rev. Lett. , vol.72 , pp. 3634-3637
    • Molgedey, L.1    Schuster, H.G.2
  • 23
    • 79953167530 scopus 로고    scopus 로고
    • Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments
    • 10.1073/pnas.1004646108
    • F. Noé, S. Doose, I. Daidone, M. Löllmann, J. D. Chodera, M. Sauer, and J. C. Smith, " Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments.," Proc. Natl. Acad. Sci. U.S.A. 108, 4822-4827 (2011). 10.1073/pnas.1004646108
    • (2011) Proc. Natl. Acad. Sci. U.S.A. , vol.108 , pp. 4822-4827
    • Noé, F.1    Doose, S.2    Daidone, I.3    Löllmann, M.4    Chodera, J.D.5    Sauer, M.6    Smith, J.C.7
  • 24
    • 34247339716 scopus 로고    scopus 로고
    • Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable states
    • 10.1063/1.2714539
    • 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). 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
  • 25
    • 84879735744 scopus 로고    scopus 로고
    • A variational approach to modeling slow processes in stochastic dynamical systems
    • 10.1137/110858616
    • F. Noé and F. Nüske, " A variational approach to modeling slow processes in stochastic dynamical systems.," SIAM Multiscale Model. Simul. 11, 635-655 (2013). 10.1137/110858616
    • (2013) SIAM Multiscale Model. Simul. , vol.11 , pp. 635-655
    • Noé, F.1    Nüske, F.2
  • 26
    • 70450255797 scopus 로고    scopus 로고
    • Constructing the full ensemble of folding pathways from short off-equilibrium simulations
    • 10.1073/pnas.0905466106
    • 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, 19011-19016 (2009). 10.1073/pnas.0905466106
    • (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
  • 27
    • 84886081379 scopus 로고    scopus 로고
    • Identification of slow molecular order parameters for Markov model construction
    • 10.1063/1.4811489
    • G. Perez-Hernandez, F. Paul, T. Giorgino, G. de Fabritiis, and Frank Noé, " Identification of slow molecular order parameters for Markov model construction.," J. Chem. Phys. 139, 015102 (2013). 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
  • 28
    • 84903370165 scopus 로고    scopus 로고
    • Spectral rate theory for projected two-state kinetics
    • (in press); e-print arXiv:1207.0225
    • J.-H. Prinz, J. D. Chodera, and F. Noé, " Spectral rate theory for projected two-state kinetics.," Phys. Rev. X (in press); e-print arXiv:1207.0225.
    • Phys. Rev. X
    • Prinz, J.-H.1    Chodera, J.D.2    Noé, F.3
  • 30
    • 0024610919 scopus 로고
    • A tutorial on hidden Markov models and selected applications in speech recognition
    • 10.1109/5.18626
    • L. R. Rabiner, " A tutorial on hidden Markov models and selected applications in speech recognition.," Proceedings of the IEEE 77, 257-286 (1989). 10.1109/5.18626
    • (1989) Proceedings of the IEEE , vol.77 , pp. 257-286
    • Rabiner, L.R.1
  • 33
    • 77956841151 scopus 로고    scopus 로고
    • On the approximation error of Markov state models
    • 10.1137/090764049
    • M. Sarich, F. Noé, and C. Schütte, " On the approximation error of Markov state models.," SIAM Multiscale Model. Simul. 8, 1154-1177 (2010). 10.1137/090764049
    • (2010) SIAM Multiscale Model. Simul. , vol.8 , pp. 1154-1177
    • Sarich, M.1    Noé, F.2    Schütte, C.3
  • 34
    • 0000573002 scopus 로고    scopus 로고
    • A direct approach to conformational dynamics based on hybrid Monte Carlo
    • 10.1006/jcph.1999.6231
    • C. Schütte, A. Fischer, W. Huisinga, and P. Deuflhard, " A direct approach to conformational dynamics based on hybrid Monte Carlo.," J. Comput. Phys. 151, 146-168 (1999). 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
  • 35
    • 84876005630 scopus 로고    scopus 로고
    • Improvements in Markov state model construction reveal many non-native interactions in the folding of NTL9
    • 10.1021/ct300878a
    • C. R. Schwantes and V. S. Pande, " Improvements in Markov state model construction reveal many non-native interactions in the folding of NTL9.," J. Chem. Theory Comput. 9, 2000-2009 (2013). 10.1021/ct300878a
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 2000-2009
    • Schwantes, C.R.1    Pande, V.S.2
  • 38
    • 28344441228 scopus 로고    scopus 로고
    • Error analysis and efficient sampling in Markovian state models for molecular dynamics
    • 10.1063/1.2116947
    • N. Singhal and V. S. Pande, " Error analysis and efficient sampling in Markovian state models for molecular dynamics.," J. Chem. Phys. 123, 204909 (2005). 10.1063/1.2116947
    • (2005) J. Chem. Phys. , vol.123 , pp. 204909
    • Singhal, N.1    Pande, V.S.2
  • 39
    • 2942560604 scopus 로고    scopus 로고
    • Describing protein folding kinetics by molecular dynamics simulations: 2. Example applications to alanine dipeptide and beta-hairpin peptide
    • 10.1021/jp037422q
    • W. C. Swope, J. W. Pitera, F. Suits, M. Pitman, and M. Eleftheriou, " Describing protein folding kinetics by molecular dynamics simulations: 2. Example applications to alanine dipeptide and beta-hairpin peptide.," J. Phys. Chem. B 108, 6582-6594 (2004). 10.1021/jp037422q
    • (2004) J. Phys. Chem. B , vol.108 , pp. 6582-6594
    • Swope, W.C.1    Pitera, J.W.2    Suits, F.3    Pitman, M.4    Eleftheriou, M.5
  • 40
    • 76149136021 scopus 로고    scopus 로고
    • Molecular simulation of ab initio protein folding for a millisecond folder NTL9
    • 10.1021/ja9090353
    • V. A. Voelz, G. R. Bowman, K. A. Beauchamp, and V. S. Pande, " Molecular simulation of ab initio protein folding for a millisecond folder NTL9.," J. Am. Chem. Soc. 132 (5), 1526-1528 (2010). 10.1021/ja9090353
    • (2010) J. Am. Chem. Soc. , vol.132 , Issue.5 , pp. 1526-1528
    • Voelz, V.A.1    Bowman, G.R.2    Beauchamp, K.A.3    Pande, V.S.4
  • 41
    • 33747589472 scopus 로고    scopus 로고
    • Towards a theory of transition paths
    • 10.1007/s10955-005-9003-9
    • W. E. and E. Vanden-Eijnden, " Towards a theory of transition paths.," J. Stat. Phys. 123 (3), 503-523 (2006). 10.1007/s10955-005-9003-9
    • (2006) J. Stat. Phys. , vol.123 , Issue.3 , pp. 503-523
    • Vanden-Eijnden, E.1
  • 43
    • 45349099441 scopus 로고    scopus 로고
    • Hidden Markov models and the Baum-Welch algorithm
    • L. R. Welch, " Hidden Markov models and the Baum-Welch algorithm.," IEEE Inf. Theory Soc. Newsl. 53, 1-13 (2003).
    • (2003) IEEE Inf. Theory Soc. Newsl. , vol.53 , pp. 1-13
    • Welch, L.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.