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Volumn 158, Issue 1, 2007, Pages 19-32

Bootstrap resampling for voxel-wise variance analysis of three-dimensional density maps derived by image analysis of two-dimensional crystals

Author keywords

Crystallography; Electron microscopy; Error analysis; Image processing; Statistics

Indexed keywords

ANALYSIS OF VARIANCE; ARTICLE; BOOTSTRAPPING; CRYSTAL; GAP JUNCTION; IMAGE ANALYSIS; JACKKNIFE TEST; PRIORITY JOURNAL; SAMPLE (STATISTICS); STANDARD; STATISTICAL ANALYSIS; STUDENT T TEST; THREE DIMENSIONAL IMAGING; VESTIBULE;

EID: 33947328020     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2006.10.003     Document Type: Article
Times cited : (16)

References (32)
  • 1
    • 0020111450 scopus 로고
    • Linking regions between helices in bacteriorhodopsin revealed
    • Agard D.A., and Stroud R.M. Linking regions between helices in bacteriorhodopsin revealed. Biophys. J. 37 (1982) 589-602
    • (1982) Biophys. J. , vol.37 , pp. 589-602
    • Agard, D.A.1    Stroud, R.M.2
  • 2
    • 70350347456 scopus 로고
    • Bootstrap methodology
    • Rao C.R. (Ed), Elsevier Science, Amsterdam
    • Babu G.J., and Rao C.R. Bootstrap methodology. In: Rao C.R. (Ed). Computational Statistics vol. 9 (1993), Elsevier Science, Amsterdam 627-659
    • (1993) Computational Statistics , vol.9 , pp. 627-659
    • Babu, G.J.1    Rao, C.R.2
  • 3
    • 0001510472 scopus 로고
    • The treatment of errors in the isomorphous replacement method
    • Blow D.M., and Crick F.H.C. The treatment of errors in the isomorphous replacement method. Acta Crystallogr. 12 (1959) 794-802
    • (1959) Acta Crystallogr. , vol.12 , pp. 794-802
    • Blow, D.M.1    Crick, F.H.C.2
  • 4
    • 0347756747 scopus 로고    scopus 로고
    • Projection structure of full length connexin 43 by electron cryo-crystallography
    • Cheng A., Schweissinger D., Dawood F., Kumar N.M., and Yeager M. Projection structure of full length connexin 43 by electron cryo-crystallography. Cell Commun. Adhes. 10 (2003) 187-191
    • (2003) Cell Commun. Adhes. , vol.10 , pp. 187-191
    • Cheng, A.1    Schweissinger, D.2    Dawood, F.3    Kumar, N.M.4    Yeager, M.5
  • 5
    • 0028103275 scopus 로고    scopus 로고
    • Collaborative Computational Project, 1994. The CCP4 Suite: Programs for protein crystallography. Acta Crystallogr. D 50, 760-763.
  • 6
    • 0015242164 scopus 로고
    • Procedures for three-dimensional reconstruction of spherical viruses by Fourier synthesis from electron micrographs
    • Crowther R.A. Procedures for three-dimensional reconstruction of spherical viruses by Fourier synthesis from electron micrographs. Philos. Trans. R. Soc. Lond. B Biol. Sci. 261 (1971) 221-230
    • (1971) Philos. Trans. R. Soc. Lond. B Biol. Sci. , vol.261 , pp. 221-230
    • Crowther, R.A.1
  • 9
    • 4444312536 scopus 로고    scopus 로고
    • Bootstrap resampling
    • El-Shaarawi A.H., and Piegorsch W.W. (Eds), Wiley, New York
    • Dixon P.M. Bootstrap resampling. In: El-Shaarawi A.H., and Piegorsch W.W. (Eds). Encyclopedia of Environmetrics vol. 1 (2002), Wiley, New York 212-219
    • (2002) Encyclopedia of Environmetrics , vol.1 , pp. 212-219
    • Dixon, P.M.1
  • 10
    • 0002344794 scopus 로고
    • Bootstrap methods: another look at the jackknife
    • Efron B. Bootstrap methods: another look at the jackknife. Ann. Stat. 7 (1979) 1-26
    • (1979) Ann. Stat. , vol.7 , pp. 1-26
    • Efron, B.1
  • 11
    • 4644228547 scopus 로고    scopus 로고
    • α model for the transmembrane α helices of gap junction intercellular channels
    • α model for the transmembrane α helices of gap junction intercellular channels. Mol. Cell 15 (2004) 879-888
    • (2004) Mol. Cell , vol.15 , pp. 879-888
    • Fleishman, S.J.1    Unger, V.M.2    Yeager, M.3    Ben-Tal, N.4
  • 13
    • 84950426508 scopus 로고
    • Bootstrapping in nonparametric regression: local adaptive smoothing and confidence bands
    • Härdle W., and Bowman A.W. Bootstrapping in nonparametric regression: local adaptive smoothing and confidence bands. J. Am. Statist. Assoc. 83 (1988) 102-110
    • (1988) J. Am. Statist. Assoc. , vol.83 , pp. 102-110
    • Härdle, W.1    Bowman, A.W.2
  • 14
    • 0039507411 scopus 로고
    • Structure of purple membrane from Halobacterium halobium: recording, measurement and evaluation of electron micrographs at 3.5 Å resolution
    • Henderson R., Baldwin J.M., Downing K.H., Lepault J., and Zemlin F. Structure of purple membrane from Halobacterium halobium: recording, measurement and evaluation of electron micrographs at 3.5 Å resolution. Ultramicroscopy 19 (1986) 147-178
    • (1986) Ultramicroscopy , vol.19 , pp. 147-178
    • Henderson, R.1    Baldwin, J.M.2    Downing, K.H.3    Lepault, J.4    Zemlin, F.5
  • 15
    • 0000895319 scopus 로고
    • The difference Fourier technique in protein crystallography: errors and their treatment
    • Henderson R., and Moffat J.K. The difference Fourier technique in protein crystallography: errors and their treatment. Acta Crystallogr. B 27 (1971) 1414-1420
    • (1971) Acta Crystallogr. B , vol.27 , pp. 1414-1420
    • Henderson, R.1    Moffat, J.K.2
  • 16
    • 0029450090 scopus 로고
    • Estimation of variance distribution in three-dimensional reconstruction. I. Theory
    • Liu W., and Frank J. Estimation of variance distribution in three-dimensional reconstruction. I. Theory. J. Opt. Soc. Am. A 12 (1995) 2615-2627
    • (1995) J. Opt. Soc. Am. A , vol.12 , pp. 2615-2627
    • Liu, W.1    Frank, J.2
  • 17
    • 0029448766 scopus 로고
    • Estimation of variance distribution in three-dimensional reconstruction. II. Applications
    • Liu W., Boisset N., and Frank J. Estimation of variance distribution in three-dimensional reconstruction. II. Applications. J. Opt. Soc. Am. A 12 (1995) 2628-2635
    • (1995) J. Opt. Soc. Am. A , vol.12 , pp. 2628-2635
    • Liu, W.1    Boisset, N.2    Frank, J.3
  • 18
    • 0023374114 scopus 로고
    • Structural relationships of actin, myosin, and tropomyosin revealed by cryo-electron microscopy
    • Milligan R.A., and Flicker P.F. Structural relationships of actin, myosin, and tropomyosin revealed by cryo-electron microscopy. J. Cell Biol. 105 (1987) 29-39
    • (1987) J. Cell Biol. , vol.105 , pp. 29-39
    • Milligan, R.A.1    Flicker, P.F.2
  • 19
    • 0027160780 scopus 로고
    • Two-dimensional crystallization of Escherichia coli-expressed bacteriorhodopsin and its D96N variant: high resolution structural studies in projection
    • Mitra A.K., Miercke L.J.W., Turner G.J., Shand R.F., Betlach M.C., and Stroud R.M. Two-dimensional crystallization of Escherichia coli-expressed bacteriorhodopsin and its D96N variant: high resolution structural studies in projection. Biophys. J. 65 (1993) 1295-1306
    • (1993) Biophys. J. , vol.65 , pp. 1295-1306
    • Mitra, A.K.1    Miercke, L.J.W.2    Turner, G.J.3    Shand, R.F.4    Betlach, M.C.5    Stroud, R.M.6
  • 20
    • 25144494760 scopus 로고    scopus 로고
    • Prediction error estimation: a comparison of resampling methods
    • Molinaro A.M., Simon R., and Pfeiffer R.M. Prediction error estimation: a comparison of resampling methods. Bioinformatics 21 (2005) 3301-3307
    • (2005) Bioinformatics , vol.21 , pp. 3301-3307
    • Molinaro, A.M.1    Simon, R.2    Pfeiffer, R.M.3
  • 21
    • 33646042904 scopus 로고    scopus 로고
    • A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation
    • Penczek P.A., Frank J., and Spahn C.M.T. A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation. J. Struct. Biol. 154 (2006) 184-194
    • (2006) J. Struct. Biol. , vol.154 , pp. 184-194
    • Penczek, P.A.1    Frank, J.2    Spahn, C.M.T.3
  • 22
    • 33644847296 scopus 로고    scopus 로고
    • Estimation of variance in single-particle reconstruction using the bootstrap technique
    • Penczek P.A., Yang C., Frank J., and Spahn C.M.T. Estimation of variance in single-particle reconstruction using the bootstrap technique. J. Struct. Biol. 154 (2006) 168-183
    • (2006) J. Struct. Biol. , vol.154 , pp. 168-183
    • Penczek, P.A.1    Yang, C.2    Frank, J.3    Spahn, C.M.T.4
  • 24
    • 0002718318 scopus 로고
    • Approximate tests of correlation in time series
    • Quenouille M.H. Approximate tests of correlation in time series. J. Roy. Statist. Soc. B 11 (1949) 68-84
    • (1949) J. Roy. Statist. Soc. B , vol.11 , pp. 68-84
    • Quenouille, M.H.1
  • 26
    • 0027190359 scopus 로고
    • Projection structure of rhodopsin
    • Schertler G.F.X., Villa C., and Henderson R. Projection structure of rhodopsin. Nature 362 (1993) 770-772
    • (1993) Nature , vol.362 , pp. 770-772
    • Schertler, G.F.X.1    Villa, C.2    Henderson, R.3
  • 27
    • 0035847002 scopus 로고    scopus 로고
    • The S-layer protein of Lactobacillus acidophilus ATCC 4356: identification and characterisation of domains responsible for S-protein assembly and cell wall binding
    • Smit E., Oling F., Demel R., Martinez B., and Pouwels P.H. The S-layer protein of Lactobacillus acidophilus ATCC 4356: identification and characterisation of domains responsible for S-protein assembly and cell wall binding. J. Mol. Biol. 305 (2001) 245-257
    • (2001) J. Mol. Biol. , vol.305 , pp. 245-257
    • Smit, E.1    Oling, F.2    Demel, R.3    Martinez, B.4    Pouwels, P.H.5
  • 29
    • 0041735000 scopus 로고    scopus 로고
    • Conformational changes in the multidrug transporter EmrE associated with substrate binding
    • Tate C.G., Ubarretxena-Belandia I., and Baldwin J.M. Conformational changes in the multidrug transporter EmrE associated with substrate binding. J. Mol. Biol. 332 (2003) 229-242
    • (2003) J. Mol. Biol. , vol.332 , pp. 229-242
    • Tate, C.G.1    Ubarretxena-Belandia, I.2    Baldwin, J.M.3
  • 30
  • 31
    • 0033582686 scopus 로고    scopus 로고
    • Three-dimensional structure of a recombinant gap junction membrane channel
    • Unger V.M., Kumar N.M., Gilula N.B., and Yeager M. Three-dimensional structure of a recombinant gap junction membrane channel. Science 283 (1999) 1176-1180
    • (1999) Science , vol.283 , pp. 1176-1180
    • Unger, V.M.1    Kumar, N.M.2    Gilula, N.B.3    Yeager, M.4
  • 32
    • 15844376311 scopus 로고    scopus 로고
    • The use of bootstrap methods for estimating sample size and analysing health-related quality of life outcomes
    • Walters S.J., and Campbell M.J. The use of bootstrap methods for estimating sample size and analysing health-related quality of life outcomes. Stat. Med. 24 (2005) 1075-1102
    • (2005) Stat. Med. , vol.24 , pp. 1075-1102
    • Walters, S.J.1    Campbell, M.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.