메뉴 건너뛰기




Volumn 119, Issue 29, 2015, Pages 9029-9037

Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models

Author keywords

[No Author keywords available]

Indexed keywords

AGGREGATES; MARKOV PROCESSES;

EID: 84937926071     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp508375q     Document Type: Article
Times cited : (100)

References (26)
  • 1
    • 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
    • (1999) J. Comput. Phys. , vol.151 , pp. 146-168
    • Schütte, C.1    Fischer, A.2    Huisinga, W.3    Deuflhard, P.4
  • 2
    • 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
    • (2004) J. Phys. Chem. B , vol.108 , pp. 6571-6581
    • Swope, W.C.1    Pitera, J.W.2    Suits, F.3
  • 3
    • 10944260594 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 9
    • 0036424048 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 17
    • 45949108535 scopus 로고    scopus 로고
    • 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 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
    • (2008) J. Phys. Chem. B , vol.112 , pp. 6057-6069
    • Buchete, N.V.1    Hummer, G.2
  • 20
    • 0001630543 scopus 로고
    • 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
  • 23
    • 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
    • (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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.