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Volumn 29, Issue 14, 2013, Pages 1750-1757

CAPITO - A web server-based analysis and plotting tool for circular dichroism data

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR DICHROISM; COMPUTER PROGRAM; INTERNET; PROCEDURES; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; ARTICLE; METHODOLOGY;

EID: 84880231834     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt278     Document Type: Article
Times cited : (190)

References (45)
  • 1
    • 0026764471 scopus 로고
    • Thermodynamic analysis of the folding of the streptococ-cal protein G IgG-binding domains B1 and B2: Why small proteins tend to have high denaturation temperatures
    • Alexander, P. et al. (1992) Thermodynamic analysis of the folding of the streptococ-cal protein G IgG-binding domains B1 and B2: why small proteins tend to have high denaturation temperatures. Biochemistry, 31, 3597-3603.
    • (1992) Biochemistry , vol.31 , pp. 3597-3603
    • Alexander, P.1
  • 2
    • 0027190754 scopus 로고
    • Evaluation of secondary structure of proteins from UV circular dichroism spectra using an unsupervised learning neural network
    • Andrade, M.A. et al. (1993) Evaluation of secondary structure of proteins from UV circular dichroism spectra using an unsupervised learning neural network. Protein Eng., 6, 383-390.
    • (1993) Protein Eng. , vol.6 , pp. 383-390
    • Andrade, M.A.1
  • 3
    • 84874499532 scopus 로고    scopus 로고
    • Solid state NMR of proteins at high MAS frequencies: Symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra
    • Bellstedt, P. et al. (2012) Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra. J. Biomol. NMR, 54, 325-335.
    • (2012) J. Biomol. NMR , vol.54 , pp. 325-335
    • Bellstedt, P.1
  • 4
    • 0033954256 scopus 로고    scopus 로고
    • The protein data bank
    • Berman, H.M. et al. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 5
    • 0026530383 scopus 로고
    • Quantitative analysis of protein far UV circular dichroism spectra by neural networks
    • Bohm, G. et al. (1992) Quantitative analysis of protein far UV circular dichroism spectra by neural networks. Protein Eng., 5, 191-195.
    • (1992) Protein Eng. , vol.5 , pp. 191-195
    • Bohm, G.1
  • 6
    • 0019005874 scopus 로고
    • Determination of protein secondary structure in solution by vacuum ultraviolet circular dichroism
    • Brahms, S. and Brahms, J. (1980) Determination of protein secondary structure in solution by vacuum ultraviolet circular dichroism. J. Mol. Biol., 138, 149-178.
    • (1980) J. Mol. Biol. , vol.138 , pp. 149-178
    • Brahms, S.1    Brahms, J.2
  • 7
    • 0015230487 scopus 로고
    • A new approach to the calculation of secondary structures of globular proteins by optical rotatory dispersion and circular di-chroism
    • Chen, Y.H. and Yang, J.T. (1971) A new approach to the calculation of secondary structures of globular proteins by optical rotatory dispersion and circular di-chroism. Biochem. Biophys. Res. Commun., 44, 1285-1291.
    • (1971) Biochem. Biophys. Res. Commun. , vol.44 , pp. 1285-1291
    • Chen, Y.H.1    Yang, J.T.2
  • 8
    • 0015522150 scopus 로고
    • Determination of the secondary structures of proteins by circular dichroism and optical rotatory dispersion
    • Chen, Y.H. et al. (1972) Determination of the secondary structures of proteins by circular dichroism and optical rotatory dispersion. Biochemistry, 11, 4120-4131.
    • (1972) Biochemistry , vol.11 , pp. 4120-4131
    • Chen, Y.H.1
  • 9
    • 0016169865 scopus 로고
    • Determination of the helix and beta form of proteins in aqueous solution by circular dichroism
    • Chen, Y.H. et al. (1974) Determination of the helix and beta form of proteins in aqueous solution by circular dichroism. Biochemistry, 13, 3350-3359.
    • (1974) Biochemistry , vol.13 , pp. 3350-3359
    • Chen, Y.H.1
  • 10
    • 0017868338 scopus 로고
    • Empirical predictions of protein conformation
    • Chou, P.Y. and Fasman, G.D. (1978) Empirical predictions of protein conformation. Annu. Rev. Biochem., 47, 251-276.
    • (1978) Annu. Rev. Biochem. , vol.47 , pp. 251-276
    • Chou, P.Y.1    Fasman, G.D.2
  • 11
    • 84915212583 scopus 로고
    • Estimation by the nearest neighbor rule
    • Cover, T.M. (1968) Estimation by the nearest neighbor rule. IEEE Trans. Information Theory, 14, 50-55.
    • (1968) IEEE Trans. Information Theory , vol.14 , pp. 50-55
    • Cover, T.M.1
  • 12
    • 0014592230 scopus 로고
    • Computed circular dichroism spectra for the evaluation of protein conformation
    • Greenfield, N. and Fasman, G.D. (1969) Computed circular dichroism spectra for the evaluation of protein conformation. Biochemistry, 8, 4108-4116.
    • (1969) Biochemistry , vol.8 , pp. 4108-4116
    • Greenfield, N.1    Fasman, G.D.2
  • 13
    • 0030042763 scopus 로고    scopus 로고
    • Methods to estimate the conformation of proteins and polypeptides from circular dichroism data
    • Greenfield, N.J. (1996) Methods to estimate the conformation of proteins and polypeptides from circular dichroism data. Anal. Biochem., 235, 1-10.
    • (1996) Anal. Biochem. , vol.235 , pp. 1-10
    • Greenfield, N.J.1
  • 14
    • 34548847733 scopus 로고    scopus 로고
    • Using circular dichroism spectra to estimate protein secondary structure
    • Greenfield, N.J. (2006) Using circular dichroism spectra to estimate protein secondary structure. Nat. Protoc., 1, 2876-2890.
    • (2006) Nat. Protoc. , vol.1 , pp. 2876-2890
    • Greenfield, N.J.1
  • 15
    • 0019871893 scopus 로고
    • Information content in the circular di-chroism of proteins
    • Hennessey, J. Jr and Johnson, W. Jr (1981) Information content in the circular di-chroism of proteins. Biochemistry, 20, 1085-1094.
    • (1981) Biochemistry , vol.20 , pp. 1085-1094
    • Hennessey, Jr.J.1    Johnson, Jr.W.2
  • 16
    • 0026703842 scopus 로고
    • Analysis of circular dichroism spectra
    • Johnson, W. Jr (1992) Analysis of circular dichroism spectra. Methods Enzymol., 210, 426-447.
    • (1992) Methods Enzymol. , vol.210 , pp. 426-447
    • Johnson, Jr.W.1
  • 17
    • 0033562629 scopus 로고    scopus 로고
    • Analyzing protein circular dichroism spectra for accurate secondary structures
    • Johnson, W.C. (1999) Analyzing protein circular dichroism spectra for accurate secondary structures. Proteins, 35, 307-312.
    • (1999) Proteins , vol.35 , pp. 307-312
    • Johnson, W.C.1
  • 18
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 19
    • 23444456924 scopus 로고    scopus 로고
    • How to study proteins by circular dichroism
    • Kelly, S.M. et al. (2005) How to study proteins by circular dichroism. Biochim. Biophys. Acta, 1751, 119-139.
    • (2005) Biochim. Biophys. Acta , vol.1751 , pp. 119-139
    • Kelly, S.M.1
  • 20
    • 84864465975 scopus 로고    scopus 로고
    • DichroMatch: A website for similarity searching of circular dichroism spectra
    • Klose, D.P. et al. (2012) DichroMatch: a website for similarity searching of circular dichroism spectra. Nucleic Acids Res., 40, W547-W552.
    • (2012) Nucleic Acids Res. , vol.40
    • Klose, D.P.1
  • 21
    • 0001757405 scopus 로고
    • The K-nearest neighbor classification rule (pattern recognition) applied to nuclear magnetic resonance spectral interpretation
    • Kowalski, B.R. and Bender, C.F. (1972) The K-nearest neighbor classification rule (pattern recognition) applied to nuclear magnetic resonance spectral interpretation. Anal. Chem., 44, 14051411.
    • (1972) Anal. Chem. , vol.44 , pp. 14051411
    • Kowalski, B.R.1    Bender, C.F.2
  • 22
    • 33747855587 scopus 로고    scopus 로고
    • A reference database for circular dichroism spectroscopy covering fold and secondary structure space
    • Lees, J.G. et al. (2006) A reference database for circular dichroism spectroscopy covering fold and secondary structure space. Bioinformatics, 22, 1955-1962.
    • (2006) Bioinformatics , vol.22 , pp. 1955-1962
    • Lees, J.G.1
  • 23
    • 84868200797 scopus 로고    scopus 로고
    • Prediction of protein secondary structure from circular dichroism using theoretically derived spectra
    • Louis Jeune, C. et al. (2012) Prediction of protein secondary structure from circular dichroism using theoretically derived spectra. Proteins, 80, 374-381.
    • (2012) Proteins , vol.80 , pp. 374-381
    • Louis Jeune, C.1
  • 24
    • 0023656828 scopus 로고
    • Variable selection method improves the prediction of protein secondary structure from circular dichroism spectra
    • Manavalan, P. and Johnson, W. Jr (1987) Variable selection method improves the prediction of protein secondary structure from circular dichroism spectra. Anal. Biochem., 167, 76-85.
    • (1987) Anal. Biochem. , vol.167 , pp. 76-85
    • Manavalan, P.1    Johnson, Jr.W.2
  • 25
    • 0020492959 scopus 로고
    • Folding of the mitochondrial proton adenosinetriphosphatase proteolipid channel in phospholipid vesicles
    • Mao, D. et al. (1982) Folding of the mitochondrial proton adenosinetriphosphatase proteolipid channel in phospholipid vesicles. Biochemistry, 21, 4960-4968.
    • (1982) Biochemistry , vol.21 , pp. 4960-4968
    • Mao, D.1
  • 26
    • 0028176595 scopus 로고
    • Measurement of the beta-sheet-forming propensities of amino acids
    • Minor, D. Jr and Kim, P.S. (1994) Measurement of the beta-sheet-forming propensities of amino acids. Nature, 367, 660-663.
    • (1994) Nature , vol.367 , pp. 660-663
    • Minor, Jr.D.1    Kim, P.S.2
  • 27
    • 0025861478 scopus 로고
    • Convex constraint analysis: A natural deconvolution of circular dichroism curves of proteins
    • Perczel, A. et al. (1991) Convex constraint analysis: a natural deconvolution of circular dichroism curves of proteins. Protein Eng., 4, 669-679.
    • (1991) Protein Eng. , vol.4 , pp. 669-679
    • Perczel, A.1
  • 28
    • 0026696116 scopus 로고
    • Analysis of the circular dichroism spectrum of proteins using the convex constraint algorithm: A practical guide
    • Perczel, A. et al. (1992a) Analysis of the circular dichroism spectrum of proteins using the convex constraint algorithm: a practical guide. Anal. Biochem., 203, 83-93.
    • (1992) Anal. Biochem. , vol.203 , pp. 83-93
    • Perczel, A.1
  • 29
    • 0026628269 scopus 로고
    • Deconvolution of the circular dichroism spectra of proteins: The circular dichroism spectra of the antiparallel beta-sheet in proteins
    • Perczel, A. et al. (1992b) Deconvolution of the circular dichroism spectra of proteins: the circular dichroism spectra of the antiparallel beta-sheet in proteins. Proteins, 13, 57-69.
    • (1992) Proteins , vol.13 , pp. 57-69
    • Perczel, A.1
  • 30
    • 0028062891 scopus 로고
    • Principal component analysis of Fourier transform infrared and/or circular dichroism spectra of proteins applied in a calibration of protein secondary structure
    • Pribicc, R. (1994) Principal component analysis of Fourier transform infrared and/or circular dichroism spectra of proteins applied in a calibration of protein secondary structure. Anal. Biochem., 223, 26-34.
    • (1994) Anal. Biochem. , vol.223 , pp. 26-34
    • Pribicc, R.1
  • 31
    • 0019873820 scopus 로고
    • Estimation of globular protein secondary structure from circular dichroism
    • Provencher, S.W. and Glockner, J. (1981) Estimation of globular protein secondary structure from circular dichroism. Biochemistry, 20, 33-37.
    • (1981) Biochemistry , vol.20 , pp. 33-37
    • Provencher, S.W.1    Glockner, J.2
  • 32
    • 0037677275 scopus 로고    scopus 로고
    • Protein concentration is not an absolute prerequisite for the determination of secondary structure from circular dichroism spectra: A new scaling method
    • Raussens, V. et al. (2003) Protein concentration is not an absolute prerequisite for the determination of secondary structure from circular dichroism spectra: a new scaling method. Anal. Biochem., 319, 114-121.
    • (2003) Anal. Biochem. , vol.319 , pp. 114-121
    • Raussens, V.1
  • 33
    • 0031543338 scopus 로고    scopus 로고
    • A set of constructed type spectra for the practical estimation of peptide secondary structure from circular dichroism
    • Reed, J. and Reed, T.A. (1997) A set of constructed type spectra for the practical estimation of peptide secondary structure from circular dichroism. Anal. Biochem., 254, 36-40.
    • (1997) Anal. Biochem. , vol.254 , pp. 36-40
    • Reed, J.1    Reed, T.A.2
  • 34
    • 0027447099 scopus 로고
    • A self-consistent method for the analysis of protein secondary structure from circular dichroism
    • Sreerama, N. and Woody, R.W. (1993) A self-consistent method for the analysis of protein secondary structure from circular dichroism. Anal. Biochem., 209, 32-44.
    • (1993) Anal. Biochem. , vol.209 , pp. 32-44
    • Sreerama, N.1    Woody, R.W.2
  • 35
    • 0034672325 scopus 로고    scopus 로고
    • Estimation of protein secondary structure from circular dichroism spectra: Comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set
    • Sreerama, N. and Woody, R.W. (2000) Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. Anal. Biochem., 287, 252-260.
    • (2000) Anal. Biochem. , vol.287 , pp. 252-260
    • Sreerama, N.1    Woody, R.W.2
  • 36
    • 1642546383 scopus 로고    scopus 로고
    • Computation and analysis of protein circular dichroism spectra
    • Sreerama, N. and Woody, R.W. (2004) Computation and analysis of protein circular dichroism spectra. Methods Enzymol., 383, 318-351.
    • (2004) Methods Enzymol. , vol.383 , pp. 318-351
    • Sreerama, N.1    Woody, R.W.2
  • 37
    • 0026599616 scopus 로고
    • Extending CD spectra of proteins to 168nm improves the analysis for secondary structures
    • Toumadje, A. et al. (1992) Extending CD spectra of proteins to 168nm improves the analysis for secondary structures. Anal. Biochem., 200, 321-331.
    • (1992) Anal. Biochem. , vol.200 , pp. 321-331
    • Toumadje, A.1
  • 38
    • 0036128797 scopus 로고    scopus 로고
    • Natively unfolded proteins: A point where biology waits for physics
    • Uversky, V.N. (2002) Natively unfolded proteins: a point where biology waits for physics. Protein Sci., 11, 739-756.
    • (2002) Protein Sci. , vol.11 , pp. 739-756
    • Uversky, V.N.1
  • 39
    • 0023652252 scopus 로고
    • Differential absorption flattening optical effects are significant in the circular dichroism spectra of large membrane fragments
    • Wallace, B.A. and Teeters, C.L. (1987) Differential absorption flattening optical effects are significant in the circular dichroism spectra of large membrane fragments. Biochemistry, 26, 65-70.
    • (1987) Biochemistry , vol.26 , pp. 65-70
    • Wallace, B.A.1    Teeters, C.L.2
  • 40
    • 30344485698 scopus 로고    scopus 로고
    • The protein circular dichroism data bank (PCDDB): A bioinformatics and spectroscopic resource
    • Wallace, B.A. et al. (2006) The protein circular dichroism data bank (PCDDB): a bioinformatics and spectroscopic resource. Proteins, 62, 1-3.
    • (2006) Proteins , vol.62 , pp. 1-3
    • Wallace, B.A.1
  • 41
    • 3242877618 scopus 로고    scopus 로고
    • DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data
    • Whitmore, L. and Wallace, B.A. (2004) DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data. Nucleic Acids Res., 32, W668-W673.
    • (2004) Nucleic Acids Res. , vol.32
    • Whitmore, L.1    Wallace, B.A.2
  • 42
    • 45849096536 scopus 로고    scopus 로고
    • Protein secondary structure analyses from circular dichroism spectroscopy: Methods and reference databases
    • Whitmore, L. and Wallace, B.A. (2008) Protein secondary structure analyses from circular dichroism spectroscopy: methods and reference databases. Biopolymers, 89, 392-400.
    • (2008) Biopolymers , vol.89 , pp. 392-400
    • Whitmore, L.1    Wallace, B.A.2
  • 43
    • 77957766588 scopus 로고    scopus 로고
    • The protein circular dichroism data bank, a Web-based site for access to circular dichroism spectroscopic data
    • Whitmore, L. et al. (2010) The protein circular dichroism data bank, a Web-based site for access to circular dichroism spectroscopic data. Structure, 18, 1267-1269.
    • (2010) Structure , vol.18 , pp. 1267-1269
    • Whitmore, L.1
  • 44
    • 78651324803 scopus 로고    scopus 로고
    • PCDDB: The protein circular dichroism data bank, a repository for circular dichroism spectral and metadata
    • Whitmore, L. et al. (2011) PCDDB: the protein circular dichroism data bank, a repository for circular dichroism spectral and metadata. Nucleic Acids Res., 39, D480-D486.
    • (2011) Nucleic Acids Res. , vol.39
    • Whitmore, L.1
  • 45
    • 0002251831 scopus 로고
    • Circular dichroism and conformation of unordered poly-pep-tides
    • Woody, R.W. (1992) Circular dichroism and conformation of unordered poly-pep-tides. Adv. Biophys. Chem., 2, 31-79.
    • (1992) Adv. Biophys. Chem. , vol.2 , pp. 31-79
    • Woody, R.W.1


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