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Volumn 21, Issue 1, 2007, Pages 59-65

Mimicking protein dynamics by the integration of elastic network model with time series analysis

Author keywords

Molecular Dynamics; Principal components analysis; Stochastic models

Indexed keywords

MATHEMATICAL MODELS; PRINCIPAL COMPONENT ANALYSIS; PROTEINS; RANDOM PROCESSES; TIME SERIES ANALYSIS;

EID: 33846660784     PISSN: 10943420     EISSN: 17412846     Source Type: Journal    
DOI: 10.1177/1094342006074861     Document Type: Conference Paper
Times cited : (1)

References (23)
  • 1
    • 26944461146 scopus 로고    scopus 로고
    • Hierarchical structure of the energy landscape of proteins revisited by time series analysis: I. Mimicking protein dynamics in different time scales
    • Alakent, B., Camurdan, M. C. and Doruker, P. (2005a). Hierarchical structure of the energy landscape of proteins revisited by time series analysis: I. Mimicking protein dynamics in different time scales. J. Chem. Phys., 123: 144910-144910.
    • (2005) J. Chem. Phys. , vol.123 , pp. 144910
    • Alakent, B.1    Camurdan, M.C.2    Doruker, P.3
  • 2
    • 26944473403 scopus 로고    scopus 로고
    • Hierarchical structure of the energy landscape of proteins revisited by time series analysis: II. Investigation of explicit solvent effects
    • Alakent, B., Camurdan, M. C. and Doruker, P. (2005b). Hierarchical structure of the energy landscape of proteins revisited by time series analysis: II. Investigation of explicit solvent effects. J. Chem. Phys., 123: 144911-144911.
    • (2005) J. Chem. Phys. , vol.123 , pp. 144911
    • Alakent, B.1    Camurdan, M.C.2    Doruker, P.3
  • 3
    • 0842311616 scopus 로고    scopus 로고
    • Time series analysis of collective motions in proteins
    • Alakent, B., Doruker, P. and Camurdan, M. C. (2004a). Time series analysis of collective motions in proteins. J. Chem. Phys., 120: 1072-1088.
    • (2004) J. Chem. Phys. , vol.120 , pp. 1072-1088
    • Alakent, B.1    Doruker, P.2    Camurdan, M.C.3
  • 4
    • 4544353149 scopus 로고    scopus 로고
    • Application of time series analysis on molecular dynamics simulations of proteins: A study of different conformational spaces by principal components analysis
    • Alakent, B., Doruker, P. and Camurdan, M. C. (2004b). Application of time series analysis on molecular dynamics simulations of proteins: A study of different conformational spaces by principal components analysis. J. Chem. Phys., 121: 4759-4769.
    • (2004) J. Chem. Phys. , vol.121 , pp. 4759-4769
    • Alakent, B.1    Doruker, P.2    Camurdan, M.C.3
  • 7
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential
    • Bahar, I., Atilgan, A. R. and Erman, B. (1997). Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential. Fold. Des. 2: 173-181.
    • (1997) Fold. Des. , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 8
    • 0031566950 scopus 로고    scopus 로고
    • Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
    • Bahar, I. and Jernigan, R. L. (1997). Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J. Mol. Biol., 266: 195-214.
    • (1997) J. Mol. Biol. , vol.266 , pp. 195-214
    • Bahar, I.1    Jernigan, R.L.2
  • 9
    • 0032483483 scopus 로고    scopus 로고
    • Vibrational dynamics of transfer RNAs. Comparison of the free and enzyme-bound forms
    • Bahar, I. and Jernigan, R. L. (1998). Vibrational dynamics of transfer RNAs. Comparison of the free and enzyme-bound forms. J. Mol. Biol., 281: 871-884.
    • (1998) J. Mol. Biol. , vol.281 , pp. 871-884
    • Bahar, I.1    Jernigan, R.L.2
  • 10
    • 0001295503 scopus 로고    scopus 로고
    • Principal component analysis and long time protein dynamics
    • Balsera, M. A., Wriggers, W., Oono, Y. and Schulten, K. (1996). Principal component analysis and long time protein dynamics. J. Phys. Chem., 100: 2567-2572.
    • (1996) J. Phys. Chem. , vol.100 , pp. 2567-2572
    • Balsera, M.A.1    Wriggers, W.2    Oono, Y.3    Schulten, K.4
  • 11
    • 0000134445 scopus 로고
    • Vibrational normal-mode spectrum of globular proteins
    • Ben-Avraham, D. (1993). Vibrational normal-mode spectrum of globular proteins. Phys. Rev. B., 47: 559-560.
    • (1993) Phys. Rev. B. , vol.47 , pp. 559-560
    • Ben-Avraham, D.1
  • 13
    • 0000991642 scopus 로고
    • Harmonic Dynamics of Proteins: Normal Modes and Fluctuations in Bovine Pancreatic Trypsin Inhibitor
    • Brooks, B. and Karplus, M. (1983). Harmonic Dynamics of Proteins: Normal Modes and Fluctuations in Bovine Pancreatic Trypsin Inhibitor. Proc. Natl. Acad. Sci. USA, 80: 6571-6575.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 6571-6575
    • Brooks, B.1    Karplus, M.2
  • 15
    • 0034663710 scopus 로고    scopus 로고
    • Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to α-amylase inhibitor
    • Doruker, P., Atilgan, A. R. and Bahar, I. (2000). Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to α-amylase inhibitor. Proteins, 40: 512-524.
    • (2000) Proteins , vol.40 , pp. 512-524
    • Doruker, P.1    Atilgan, A.R.2    Bahar, I.3
  • 16
    • 0141815545 scopus 로고    scopus 로고
    • Functional motions can be extracted from on-lattice construction of protein structures
    • Doruker, P. and Jernigan, R. L. (2003). Functional motions can be extracted from on-lattice construction of protein structures. Protein, 53: 174-181.
    • (2003) Protein , vol.53 , pp. 174-181
    • Doruker, P.1    Jernigan, R.L.2
  • 17
    • 0020771265 scopus 로고
    • Dynamics of a small globular protein in terms of low-frequency vibrational modes
    • Go, N., Noguti, T. and Nishikawa, T. (1983). Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. USA, 80: 3696-3700.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 3696-3700
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 18
    • 0000689085 scopus 로고
    • Predicting slow structural transitions in macromolecular systems: Conformational flooding
    • Grubmüller, H. (1995). Predicting slow structural transitions in macromolecular systems: Conformational flooding. Phys. Rev. E, 52: 2893-2906.
    • (1995) Phys. Rev. E , vol.52 , pp. 2893-2906
    • Grubmüller, H.1
  • 19
    • 0027732618 scopus 로고
    • Effect of solvent on collective motions in globular proteins
    • Hayward, S., Kitao, A. and Go, N. (1993). Effect of solvent on collective motions in globular proteins. J. Mol. Biol., 234: 1207-1217.
    • (1993) J. Mol. Biol. , vol.234 , pp. 1207-1217
    • Hayward, S.1    Kitao, A.2    Go, N.3
  • 20
    • 0033117937 scopus 로고    scopus 로고
    • Investigating protein dynamics in collective coordinate space
    • Kitao, A. and Go, N. (1999). Investigating protein dynamics in collective coordinate space. Curr. Opin. Struct. Biol., 9: 164-169.
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 164-169
    • Kitao, A.1    Go, N.2
  • 21
    • 0000998079 scopus 로고
    • The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulation of mellitin in water and in vacuum
    • Kitao, A., Hirata, F. and Go, N. (1991). The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulation of mellitin in water and in vacuum. J. Chem. Phys., 158: 447-472.
    • (1991) J. Chem. Phys. , vol.158 , pp. 447-472
    • Kitao, A.1    Hirata, F.2    Go, N.3
  • 22
    • 4344685227 scopus 로고    scopus 로고
    • Global ribosome motions revealed by elastic network model
    • Wang, Y., Rader, A. J., Bahar, I. and Jernigan, R. L. (2004). Global ribosome motions revealed by elastic network model. J. Struc. Biol., 147: 302-314.
    • (2004) J. Struc. Biol. , vol.147 , pp. 302-314
    • Wang, Y.1    Rader, A.J.2    Bahar, I.3    Jernigan, R.L.4
  • 23
    • 8444243746 scopus 로고    scopus 로고
    • Collective motions of RNA polymerases. Analysis of core enzyme, elongation complex and holoenzyme
    • Yildirim, Y. and Doruker, P. (2004). Collective motions of RNA polymerases. Analysis of core enzyme, elongation complex and holoenzyme. J. Biomol. Struc. Dyn., 22: 267-280.
    • (2004) J. Biomol. Struc. Dyn. , vol.22 , pp. 267-280
    • Yildirim, Y.1    Doruker, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.