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Volumn 103, Issue 6, 1999, Pages 909-911

Stochastic path approach to compute atomically detailed trajectories: Application to the folding of C peptide

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EID: 16444370098     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp983774z     Document Type: Article
Times cited : (88)

References (34)
  • 2
    • 0026526264 scopus 로고
    • Distal Pocket Residues Affect Picosecond Recombination in Myoglobin: An experimental and Molecular Dynamics Study of Position 29 Mutants
    • Gibson, Q. H.; Regan, R.; Elber, R.; Olson, J. S.; Carver, T. E. Distal Pocket Residues Affect Picosecond Recombination in Myoglobin: An experimental and Molecular Dynamics Study of Position 29 Mutants. J. Biol. Chem. 1992, 267, 22022.
    • (1992) J. Biol. Chem. , vol.267 , pp. 22022
    • Gibson, Q.H.1    Regan, R.2    Elber, R.3    Olson, J.S.4    Carver, T.E.5
  • 3
    • 0027202194 scopus 로고
    • Molecular Dynamics Simulations of NO Recombination to Myoglobin mutants
    • Li, H.; Elber, R.; Straub, J. E. Molecular Dynamics Simulations of NO Recombination to Myoglobin mutants. J. Biol. Chem. 1993, 268, 17908.
    • (1993) J. Biol. Chem. , vol.268 , pp. 17908
    • Li, H.1    Elber, R.2    Straub, J.E.3
  • 4
    • 0031587288 scopus 로고    scopus 로고
    • Kinetics of Peptide Folding: Computer Simulations of SYPFDV and peptide variants in water
    • Mohanty, D.; Elber, R.; Thirumalai, D.; Beglov, D.; Roux, R. Kinetics of Peptide Folding: Computer Simulations of SYPFDV and peptide variants in water. J. Mol. Biol. 1997, 272, 423-442.
    • (1997) J. Mol. Biol. , vol.272 , pp. 423-442
    • Mohanty, D.1    Elber, R.2    Thirumalai, D.3    Beglov, D.4    Roux, R.5
  • 7
    • 0012021417 scopus 로고    scopus 로고
    • Calculation of Classical Trajectories with a Very Large Time Step: Formalism and Numerical Examples
    • Olender, R.; Elber, R. Calculation of Classical Trajectories with a Very Large Time Step: Formalism and Numerical Examples. J. Chem. Phys. 1996, 105, 9299-9315.
    • (1996) J. Chem. Phys. , vol.105 , pp. 9299-9315
    • Olender, R.1    Elber, R.2
  • 13
    • 0004206591 scopus 로고
    • University of Toronto Press: Toronto
    • i (private communication). The Gauss variation principle can be found in the following: Lanczos, C. The Variational Principles of Mechanics; University of Toronto Press: Toronto, 1970.
    • (1970) The Variational Principles of Mechanics
    • Lanczos, C.1
  • 16
    • 36149007093 scopus 로고
    • Onsager, L.; Machlup, S. Phys. Rev. 1953, 91, 1505; 1953, 97,1512.
    • (1953) Phys. Rev. , vol.97 , pp. 1512
  • 17
    • 0000055722 scopus 로고
    • Diffusion-controlled reactions: A variational formula for optimum reaction coordinate
    • Berkowitz, M.; Morgan, J. D.; McCammon, J. A.; Northrup, S. H. Diffusion-controlled reactions: A variational formula for optimum reaction coordinate. J. Chem. Phys. 1983, 79, 5563-5565.
    • (1983) J. Chem. Phys. , vol.79 , pp. 5563-5565
    • Berkowitz, M.1    Morgan, J.D.2    McCammon, J.A.3    Northrup, S.H.4
  • 20
    • 4243691221 scopus 로고    scopus 로고
    • Yet another look at the Steepest Descent Path
    • Olender, R.; Elber, R. Yet another look at the Steepest Descent Path. J. Mol. Struct. (THEOCHEM) 1997, 398/399, 63-72.
    • (1997) J. Mol. Struct. (THEOCHEM) , vol.398-399 , pp. 63-72
    • Olender, R.1    Elber, R.2
  • 21
    • 0000729781 scopus 로고    scopus 로고
    • Transition Path Sampling and the Calculation of Rate Constants
    • Dellago, C.; Bolhuis, P. G.; Csajka, F. S.; Chandler, D. Transition Path Sampling and the Calculation of Rate Constants. J. Chem. Phys. 1998, 108, 1964-1977. Csajka, F. S.; Chandler, D. Transition Pathways in many-body system: Application to hydrogen-bond breaking in water. J. Chem. Phys. 1998, 109, 1125-1133.
    • (1998) J. Chem. Phys. , vol.108 , pp. 1964-1977
    • Dellago, C.1    Bolhuis, P.G.2    Csajka, F.S.3    Chandler, D.4
  • 22
    • 0000320320 scopus 로고    scopus 로고
    • Transition Pathways in many-body system: Application to hydrogen-bond breaking in water
    • Dellago, C.; Bolhuis, P. G.; Csajka, F. S.; Chandler, D. Transition Path Sampling and the Calculation of Rate Constants. J. Chem. Phys. 1998, 108, 1964-1977. Csajka, F. S.; Chandler, D. Transition Pathways in many-body system: Application to hydrogen-bond breaking in water. J. Chem. Phys. 1998, 109, 1125-1133.
    • (1998) J. Chem. Phys. , vol.109 , pp. 1125-1133
    • Csajka, F.S.1    Chandler, D.2
  • 23
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys. 1977, 23, 327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 24
    • 48749148224 scopus 로고
    • Rattle: A velocity version of the SHAKE algorithm for molecular dynamics calculations
    • Andersen, H. C. Rattle: a velocity version of the SHAKE algorithm for molecular dynamics calculations. J. Comput. Phys. 1983, 52, 24-34.
    • (1983) J. Comput. Phys. , vol.52 , pp. 24-34
    • Andersen, H.C.1
  • 26
    • 0003023614 scopus 로고
    • MOIL-View - A Program for Visualization of Structure and Dynamics of Biomolecules and STO - a Program for Computation of Stochastic Paths
    • Pullman, A., Ed.; Kulwer Academic Publishers: Netherlands
    • Simmerling, C.; Elber, R.; Zhang, J. MOIL-View - a Program for Visualization of Structure and Dynamics of Biomolecules and STO - A Program for Computation of Stochastic Paths. In The Proceeding of the Jerusalem Symposium on Theoretical Biochemistry; Pullman, A., Ed.; Kulwer Academic Publishers: Netherlands, 1995; pp 241-265.
    • (1995) The Proceeding of the Jerusalem Symposium on Theoretical Biochemistry , pp. 241-265
    • Simmerling, C.1    Elber, R.2    Zhang, J.3
  • 31
    • 0024472052 scopus 로고    scopus 로고
    • Proton NMR studies of the solution conformations of an analog of the C-peptide of Ribonuclease A
    • Osterhout, J. J.; Baldwin, R. L.; York, E. J.; Stewart, J. M.; Dyson, J. H.; Wright, P. E. Proton NMR studies of the solution conformations of an analog of the C-peptide of Ribonuclease A. Biochemistry 1998, 28, 7059-7064.
    • (1998) Biochemistry , vol.28 , pp. 7059-7064
    • Osterhout, J.J.1    Baldwin, R.L.2    York, E.J.3    Stewart, J.M.4    Dyson, J.H.5    Wright, P.E.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.