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Volumn 78, Issue 1, 2000, Pages 136-149

Nonlinear methods in the analysis of protein sequences: A case study in rubredoxins

Author keywords

[No Author keywords available]

Indexed keywords

RUBREDOXIN;

EID: 0034083950     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(00)76580-5     Document Type: Article
Times cited : (53)

References (44)
  • 1
    • 85120121594 scopus 로고    scopus 로고
    • Oxidoreductase-Type Enzymes and Redox Proteins Involved in Fermentative Metabolisms of Hyperthermophilic Archaea
    • M.W.W. Adams A. Keltzin Oxidoreductase-Type Enzymes and Redox Proteins Involved in Fermentative Metabolisms of Hyperthermophilic Archaea F.M. Richards D.S. Eisenberg P.S. Kim Advances in Protein Chemistry 48 1996 Academic Press New York
    • (1996)
    • Adams, M.W.W.1    Keltzin, A.2
  • 2
    • 0004292021 scopus 로고
    • Cluster Analysis for Applications
    • M.R. Anderberg Cluster Analysis for Applications 1973 Academic Press New York
    • (1973)
    • Anderberg, M.R.1
  • 3
    • 0015859467 scopus 로고
    • Principles that govern the folding of proteins
    • C.B. Anfinsen Principles that govern the folding of proteins Science 181 1973 223 230
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 4
    • 34249988665 scopus 로고
    • Extracting qualitative dynamics from experimental data
    • D.S. Broomhead G.P. King Extracting qualitative dynamics from experimental data Physica D 20 1986 217 236
    • (1986) Physica D , vol.20 , pp. 217-236
    • Broomhead, D.S.1    King, G.P.2
  • 5
    • 85120124392 scopus 로고
    • M.O. Dayhoff R.M. Schwartz B.C. Orcutt M.O. Dayhoff Atlas of Protein Sequence and Structure 5 1978 NBRF Washington 345 supplement 3
    • (1978) , pp. 345
    • Dayhoff, M.O.1    Schwartz, R.M.2    Orcutt, B.C.3
  • 7
    • 0030808566 scopus 로고    scopus 로고
    • Dissecting contributions to the thermostability of Pyrococcus furiosus rubredoxin: sheet chimeras
    • M. Eidsness K.A. Richie A.E. Burden D.M. Kurtz R.A. Scott Dissecting contributions to the thermostability of Pyrococcus furiosus rubredoxin: sheet chimeras Biochemistry 36 1997 10406 10413
    • (1997) Biochemistry , vol.36 , pp. 10406-10413
    • Eidsness, M.1    Richie, K.A.2    Burden, A.E.3    Kurtz, D.M.4    Scott, R.A.5
  • 8
    • 0030911801 scopus 로고    scopus 로고
    • A nonrandom dynamic component in the synaptic noise of a central neuron
    • P. Faure H. Korn A nonrandom dynamic component in the synaptic noise of a central neuron Proc. R. Soc. London Ser. A. Natl. Acad. Sci. USA 94 1997 6506 6511
    • (1997) Proc. R. Soc. London Ser. A. Natl. Acad. Sci. USA , vol.94 , pp. 6506-6511
    • Faure, P.1    Korn, H.2
  • 9
    • 0003561150 scopus 로고
    • Theoretical Drug Design Methods
    • R. Franke Theoretical Drug Design Methods 1984 Elsevier Amsterdam
    • (1984)
    • Franke, R.1
  • 10
    • 0000013976 scopus 로고    scopus 로고
    • Hidden peculiarities in the potential energy time series of a tripeptide highlighted by a recurrence plot analysis: a molecular dynamics simulation
    • A. Giuliani C. Manetti Hidden peculiarities in the potential energy time series of a tripeptide highlighted by a recurrence plot analysis: a molecular dynamics simulation Phys. Rev. E 53 1996 6336 6340
    • (1996) Phys. Rev. E , vol.53 , pp. 6336-6340
    • Giuliani, A.1    Manetti, C.2
  • 11
    • 33750869200 scopus 로고    scopus 로고
    • A nonlinear explanation of aging-induced changes in heartbeat dynamics
    • A. Giuliani G. Piccirillo V. Marigliano A. Colosimo A nonlinear explanation of aging-induced changes in heartbeat dynamics Am. J. Physiol. 275 1998 H1455 H1461
    • (1998) Am. J. Physiol. , vol.275 , pp. H1455-H1461
    • Giuliani, A.1    Piccirillo, G.2    Marigliano, V.3    Colosimo, A.4
  • 12
    • 0001059812 scopus 로고
    • Quantitative structure-activity relationships and the unnamed science
    • C. Hansch Quantitative structure-activity relationships and the unnamed science Account. Chem. Res. 26 1993 147 153
    • (1993) Account. Chem. Res. , vol.26 , pp. 147-153
    • Hansch, C.1
  • 13
    • 0000652554 scopus 로고    scopus 로고
    • Comparative QSAR: toward a deeper understanding of chemicobiological interactions
    • C. Hansch D. Hoekman H. Gao Comparative QSAR: toward a deeper understanding of chemicobiological interactions Chem. Rev. 96 1996 1045 1075
    • (1996) Chem. Rev. , vol.96 , pp. 1045-1075
    • Hansch, C.1    Hoekman, D.2    Gao, H.3
  • 14
    • 0003955925 scopus 로고
    • Exploring QSAR: Fundamentals and Applications in Chemistry and Biology
    • C. Hansch A. Leo Exploring QSAR: Fundamentals and Applications in Chemistry and Biology 1995 American Chemical Society Washington DC.
    • (1995)
    • Hansch, C.1    Leo, A.2
  • 15
    • 34447521097 scopus 로고
    • Correlation of biological activity of phenoxyacetic acids with Hammett substituent constants and partition coefficients
    • C. Hansch P.P. Maloney T. Fujita R. Muir Correlation of biological activity of phenoxyacetic acids with Hammett substituent constants and partition coefficients Nature 194 1962 178 180
    • (1962) Nature , vol.194 , pp. 178-180
    • Hansch, C.1    Maloney, P.P.2    Fujita, T.3    Muir, R.4
  • 16
    • 0003406531 scopus 로고
    • Modern Factor Analysis
    • H. Harman Modern Factor Analysis 3rd Ed 1976 Chicago University Press Chicago
    • (1976)
    • Harman, H.1
  • 17
    • 0024598146 scopus 로고
    • Fast and sensitive multiple sequence alignments on a microcomputer
    • D.G. Higgins P.M. Sharp Fast and sensitive multiple sequence alignments on a microcomputer Comp. Appl. Biosci. 5 1989 151 153
    • (1989) Comp. Appl. Biosci. , vol.5 , pp. 151-153
    • Higgins, D.G.1    Sharp, P.M.2
  • 18
    • 35949011257 scopus 로고
    • Easily calculable measure for the complexity of spatiotemporal patterns
    • F. Kaspar K.G. Schuster Easily calculable measure for the complexity of spatiotemporal patterns Phys. Rev. A 36 1987 842 847
    • (1987) Phys. Rev. A , vol.36 , pp. 842-847
    • Kaspar, F.1    Schuster, K.G.2
  • 19
    • 0004046696 scopus 로고
    • The Neutral Theory of Molecular Evolution
    • M. Kimura The Neutral Theory of Molecular Evolution 1983 Cambridge University Press Cambridge, UK
    • (1983)
    • Kimura, M.1
  • 20
    • 0001996854 scopus 로고
    • Molecular Modeling
    • T.F. Kumosinski M.N. Liebman Molecular Modeling 1994 American Chemical Society Washington, DC.
    • (1994)
    • Kumosinski, T.F.1    Liebman, M.N.2
  • 21
    • 7044220745 scopus 로고    scopus 로고
    • Nature of driving force for protein folding: a result from analyzing the statistical potential
    • H. Li C. Tang N.S. Wingreen Nature of driving force for protein folding: a result from analyzing the statistical potential Phys. Rev. Lett. 79 1997 765 768
    • (1997) Phys. Rev. Lett. , vol.79 , pp. 765-768
    • Li, H.1    Tang, C.2    Wingreen, N.S.3
  • 23
    • 0031443422 scopus 로고    scopus 로고
    • Mode matches and their locations in the hydrophobic free energy sequences of peptide ligands and their receptor eigenfunctions
    • A.J. Mandell K. Selz M.F. Shlesinger Mode matches and their locations in the hydrophobic free energy sequences of peptide ligands and their receptor eigenfunctions Proc. R. Soc. London Ser. A. Natl. Acad. Sci. USA 94 1997 13576 13581
    • (1997) Proc. R. Soc. London Ser. A. Natl. Acad. Sci. USA , vol.94 , pp. 13576-13581
    • Mandell, A.J.1    Selz, K.2    Shlesinger, M.F.3
  • 24
    • 0001649140 scopus 로고    scopus 로고
    • Recurrence quantification analysis as a tool for characterization of molecular dynamics simulations
    • C. Manetti M.A. Ceruso A. Giuliani C.L. Webber Jr. J.P. Zbilut Recurrence quantification analysis as a tool for characterization of molecular dynamics simulations Phys. Rev. E 59 1999 992 998
    • (1999) Phys. Rev. E , vol.59 , pp. 992-998
    • Manetti, C.1    Ceruso, M.A.2    Giuliani, A.3    Webber, C.L.4    Zbilut, J.P.5
  • 25
    • 0019422355 scopus 로고
    • A practitioner's perspective of the role of quantitative structure-activity analysis in medicinal chemistry
    • Y. Martin A practitioner's perspective of the role of quantitative structure-activity analysis in medicinal chemistry J. Med. Chem. 24 1981 229 237
    • (1981) J. Med. Chem. , vol.24 , pp. 229-237
    • Martin, Y.1
  • 26
    • 0000823682 scopus 로고    scopus 로고
    • Protein design in a lattice model of hydrophobic and polar amino acids
    • C. Micheletti F. Senno A. Maritan J.R. Banavar Protein design in a lattice model of hydrophobic and polar amino acids Phys. Rev. Lett. 80 1998 2237 2240
    • (1998) Phys. Rev. Lett. , vol.80 , pp. 2237-2240
    • Micheletti, C.1    Senno, F.2    Maritan, A.3    Banavar, J.R.4
  • 27
    • 0033150835 scopus 로고    scopus 로고
    • Sequences and topology. From sequence to structure to function
    • A.G. Murzin L. Patthy Sequences and topology. From sequence to structure to function Curr. Opin. Struct. Biol. 9 1999 359 362
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 359-362
    • Murzin, A.G.1    Patthy, L.2
  • 28
    • 0030203863 scopus 로고    scopus 로고
    • TREEVIEW: an application to display phylogenetic trees on personal computers
    • R.D.M. Page TREEVIEW: an application to display phylogenetic trees on personal computers Comp. Appl. Biosci. 12 1996 357 358
    • (1996) Comp. Appl. Biosci. , vol.12 , pp. 357-358
    • Page, R.D.M.1
  • 30
    • 0023375195 scopus 로고
    • The neighbor-joining method: a new method for reconstructing phylogenetic trees
    • N. Saitou M. Nei The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol. Biol. Evol. 4 1987 406 425
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 31
    • 0031722678 scopus 로고    scopus 로고
    • Hydrophobic free energy eigenfunctions of pore, channel, and transporter proteins contain beta-burst patterns
    • K.A. Selz A.J. Mandell M.F. Shlesinger Hydrophobic free energy eigenfunctions of pore, channel, and transporter proteins contain beta-burst patterns Biophys. J. 75 1998 2332 2342
    • (1998) Biophys. J. , vol.75 , pp. 2332-2342
    • Selz, K.A.1    Mandell, A.J.2    Shlesinger, M.F.3
  • 33
    • 0004069901 scopus 로고
    • Numerical Taxonomy
    • P.H.A. Sneath R.R. Sokal Numerical Taxonomy 1973 Freeman San Francisco
    • (1973)
    • Sneath, P.H.A.1    Sokal, R.R.2
  • 34
    • 0029938188 scopus 로고    scopus 로고
    • The Shannon information entropy of protein sequences
    • B.J. Strait T.G. Dewey The Shannon information entropy of protein sequences Biophys. J. 71 1996 148 155
    • (1996) Biophys. J. , vol.71 , pp. 148-155
    • Strait, B.J.1    Dewey, T.G.2
  • 35
    • 0021112868 scopus 로고
    • Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure
    • R.M. Sweet D. Eisenberg Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure J. Mol. Biol. 171 1983 479 488
    • (1983) J. Mol. Biol. , vol.171 , pp. 479-488
    • Sweet, R.M.1    Eisenberg, D.2
  • 36
    • 0031574072 scopus 로고    scopus 로고
    • The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
    • J.D. Thompson T.J. Gibson F. Plewniak F. Jeanmougin D.G. Higgins The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res. 25 1997 4876 4882
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 37
    • 13544249190 scopus 로고    scopus 로고
    • Recurrence quantification analysis of the logistic equation with transients
    • L.L. Trulla A. Giuliani J.P. Zbilut C.L. Webber Recurrence quantification analysis of the logistic equation with transients Phys. Lett. A 223 1996 255 260
    • (1996) Phys. Lett. A , vol.223 , pp. 255-260
    • Trulla, L.L.1    Giuliani, A.2    Zbilut, J.P.3    Webber, C.L.4
  • 38
    • 0020483698 scopus 로고
    • Signal sequences are not uniformly hydrophobic
    • G. von Heijne Signal sequences are not uniformly hydrophobic J. Mol. Biol. 159 1982 537 541
    • (1982) J. Mol. Biol. , vol.159 , pp. 537-541
    • von Heijne, G.1
  • 39
    • 0028354598 scopus 로고
    • Dynamical assessment of physiological systems and states using recurrence plot strategies
    • C.L. Webber J.P. Zbilut Dynamical assessment of physiological systems and states using recurrence plot strategies J. Appl. Physiol. 76 1994 965 973
    • (1994) J. Appl. Physiol. , vol.76 , pp. 965-973
    • Webber, C.L.1    Zbilut, J.P.2
  • 40
    • 0032554318 scopus 로고    scopus 로고
    • Correlations in protein sequences and property codes J
    • O. Weiss H. Herzel Correlations in protein sequences and property codes J Theor. Biol. 190 4 1998 341 353
    • (1998) Theor. Biol. , vol.190 , Issue.4 , pp. 341-353
    • Weiss, O.1    Herzel, H.2
  • 42
    • 0042357254 scopus 로고    scopus 로고
    • Recurrence quantification analysis and principal components in the detection of short complex signals
    • J.P. Zbilut A. Giuliani C.L. Webber Recurrence quantification analysis and principal components in the detection of short complex signals Phys. Lett. A 237 1998 131 135
    • (1998) Phys. Lett. A , vol.237 , pp. 131-135
    • Zbilut, J.P.1    Giuliani, A.2    Webber, C.L.3
  • 43
    • 0031918921 scopus 로고    scopus 로고
    • Recurrence quantification analysis in structure-function relationships of proteins: an overview of a general methodology applied to the case of TEM-1 beta-lactamase
    • J.P. Zbilut A. Giuliani C.L. Webber A. Colosimo Recurrence quantification analysis in structure-function relationships of proteins: an overview of a general methodology applied to the case of TEM-1 beta-lactamase Protein Eng. 11 1998 87 93
    • (1998) Protein Eng. , vol.11 , pp. 87-93
    • Zbilut, J.P.1    Giuliani, A.2    Webber, C.L.3    Colosimo, A.4
  • 44
    • 0000688735 scopus 로고
    • Embeddings and delays as derived from quantification of recurrence plots
    • J.P. Zbilut C.L. Webber Embeddings and delays as derived from quantification of recurrence plots Phys. Lett. A 171 1992 199 203
    • (1992) Phys. Lett. A , vol.171 , pp. 199-203
    • Zbilut, J.P.1    Webber, C.L.2


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