메뉴 건너뛰기




Volumn 6, Issue SUPPL.1, 2012, Pages

High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ELECTRON TOMOGRAPHY; FOURIER ANALYSIS; IMAGE PROCESSING; IMAGE QUALITY; METHODOLOGY; PROTEIN DATABASE; SIGNAL NOISE RATIO; STATISTICS;

EID: 84875810072     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-S1-S18     Document Type: Article
Times cited : (18)

References (35)
  • 4
    • 70350709997 scopus 로고    scopus 로고
    • Visual proteomics of the human pathogen Leptospira interrogans
    • 10.1038/nmeth.1390, 2862215, 19838170
    • Beck M, Malmström J, Lange V, Schmidt A, Deutsch E, Aebersold R. Visual proteomics of the human pathogen Leptospira interrogans. Nature methods 2009, 6(11):817-823. 10.1038/nmeth.1390, 2862215, 19838170.
    • (2009) Nature methods , vol.6 , Issue.11 , pp. 817-823
    • Beck, M.1    Malmström, J.2    Lange, V.3    Schmidt, A.4    Deutsch, E.5    Aebersold, R.6
  • 5
    • 79851514947 scopus 로고    scopus 로고
    • Exploring the Spatial and Temporal Organization of a Cell's Proteome
    • 10.1016/j.jsb.2010.11.011, 21094684
    • Beck M, Topf M, Frazier Z, Tjong H, Xu M, Zhang S, Alber F. Exploring the Spatial and Temporal Organization of a Cell's Proteome. Journal of Structural Biology 2011, 173(3):483-496. 10.1016/j.jsb.2010.11.011, 21094684.
    • (2011) Journal of Structural Biology , vol.173 , Issue.3 , pp. 483-496
    • Beck, M.1    Topf, M.2    Frazier, Z.3    Tjong, H.4    Xu, M.5    Zhang, S.6    Alber, F.7
  • 6
    • 79959477905 scopus 로고    scopus 로고
    • Template-free detection of macromolecular complexes in cryo electron tomograms
    • 10.1093/bioinformatics/btr207, 3117359, 21685103
    • Xu M, Beck M, Alber F. Template-free detection of macromolecular complexes in cryo electron tomograms. Bioinformatics 2011, 27(13):i69-i76. 10.1093/bioinformatics/btr207, 3117359, 21685103.
    • (2011) Bioinformatics , vol.27 , Issue.13
    • Xu, M.1    Beck, M.2    Alber, F.3
  • 9
    • 50649105102 scopus 로고    scopus 로고
    • Toward a biomechanical understanding of whole bacterial cells
    • 10.1146/annurev.biochem.77.061206.173846, 18355161
    • Morris D, Jensen G. Toward a biomechanical understanding of whole bacterial cells. Annu Rev Biochem 2008, 77:583-613. 10.1146/annurev.biochem.77.061206.173846, 18355161.
    • (2008) Annu Rev Biochem , vol.77 , pp. 583-613
    • Morris, D.1    Jensen, G.2
  • 10
    • 0043237770 scopus 로고    scopus 로고
    • Image registration methods: a survey
    • Zitova B, Flusser J. Image registration methods: a survey. Image and vision computing 2003, 21(11):977-1000.
    • (2003) Image and vision computing , vol.21 , Issue.11 , pp. 977-1000
    • Zitova, B.1    Flusser, J.2
  • 11
    • 40649128324 scopus 로고    scopus 로고
    • Classification of cryo-electron sub-tomograms using constrained correlation
    • 10.1016/j.jsb.2007.07.006, 17720536
    • Förster F, Pruggnaller S, Seybert A, Frangakis A. Classification of cryo-electron sub-tomograms using constrained correlation. Journal of structural biology 2008, 161(3):276-286. 10.1016/j.jsb.2007.07.006, 17720536.
    • (2008) Journal of structural biology , vol.161 , Issue.3 , pp. 276-286
    • Förster, F.1    Pruggnaller, S.2    Seybert, A.3    Frangakis, A.4
  • 12
    • 77955086484 scopus 로고    scopus 로고
    • Subtomogram alignment by adaptive Fourier coefficient thresholding
    • 10.1016/j.jsb.2010.05.013, 20621702
    • Amat F, Comolli L, Moussavi F, Smit J, Downing K, Horowitz M. Subtomogram alignment by adaptive Fourier coefficient thresholding. Journal of structural biology 2010, 171(3):332-344. 10.1016/j.jsb.2010.05.013, 20621702.
    • (2010) Journal of structural biology , vol.171 , Issue.3 , pp. 332-344
    • Amat, F.1    Comolli, L.2    Moussavi, F.3    Smit, J.4    Downing, K.5    Horowitz, M.6
  • 13
    • 84860584901 scopus 로고    scopus 로고
    • PyTom: A python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis
    • 10.1016/j.jsb.2011.12.003, 22193517
    • Hrabe T, Chen Y, Pfeffer S, Kuhn Cuellar L, Mangold A, Förster F. PyTom: A python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis. Journal of structural biology 2012, 178(2):177-188. 10.1016/j.jsb.2011.12.003, 22193517.
    • (2012) Journal of structural biology , vol.178 , Issue.2 , pp. 177-188
    • Hrabe, T.1    Chen, Y.2    Pfeffer, S.3    Kuhn Cuellar, L.4    Mangold, A.5    Förster, F.6
  • 14
    • 44449179947 scopus 로고    scopus 로고
    • Classification and 3D averaging with missing wedge correction in biological electron tomography
    • 10.1016/j.jsb.2008.02.008, 2556382, 18440828
    • Bartesaghi A, Sprechmann P, Liu J, Randall G, Sapiro G, Subramaniam S. Classification and 3D averaging with missing wedge correction in biological electron tomography. Journal of structural biology 2008, 162(3):436-450. 10.1016/j.jsb.2008.02.008, 2556382, 18440828.
    • (2008) Journal of structural biology , vol.162 , Issue.3 , pp. 436-450
    • Bartesaghi, A.1    Sprechmann, P.2    Liu, J.3    Randall, G.4    Sapiro, G.5    Subramaniam, S.6
  • 15
    • 84860594033 scopus 로고    scopus 로고
    • High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching
    • 10.1016/j.jsb.2012.02.014, 22420977
    • Xu M, Beck M, Alber F. High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching. Journal of structural biology 2012, 178(2):152-164. 10.1016/j.jsb.2012.02.014, 22420977.
    • (2012) Journal of structural biology , vol.178 , Issue.2 , pp. 152-164
    • Xu, M.1    Beck, M.2    Alber, F.3
  • 16
    • 77957278883 scopus 로고    scopus 로고
    • Methods for segmentation and interpretation of electron tomographic reconstructions
    • Volkmann N. Methods for segmentation and interpretation of electron tomographic reconstructions. Methods Enzymol 2010, 483:31-46.
    • (2010) Methods Enzymol , vol.483 , pp. 31-46
    • Volkmann, N.1
  • 17
    • 40649109028 scopus 로고    scopus 로고
    • Methods for aligning and for averaging 3D volumes with missing data
    • 10.1016/j.jsb.2007.09.018, 2680136, 18299206
    • Schmid M, Booth C. Methods for aligning and for averaging 3D volumes with missing data. Journal of structural biology 2008, 161(3):243-248. 10.1016/j.jsb.2007.09.018, 2680136, 18299206.
    • (2008) Journal of structural biology , vol.161 , Issue.3 , pp. 243-248
    • Schmid, M.1    Booth, C.2
  • 18
    • 0031423486 scopus 로고    scopus 로고
    • Electron tomography of single ice-embedded macromolecules: three-dimensional alignment and classification
    • 10.1006/jsbi.1997.3934, 9441941
    • Walz J, Typke D, Nitsch M, Koster A, Hegerl R, Baumeister W. Electron tomography of single ice-embedded macromolecules: three-dimensional alignment and classification. Journal of structural biology 1997, 120(3):387-395. 10.1006/jsbi.1997.3934, 9441941.
    • (1997) Journal of structural biology , vol.120 , Issue.3 , pp. 387-395
    • Walz, J.1    Typke, D.2    Nitsch, M.3    Koster, A.4    Hegerl, R.5    Baumeister, W.6
  • 19
    • 33845310367 scopus 로고    scopus 로고
    • 3D reconstruction and processing of volumetric data incryo-electron tomography
    • 10.1016/j.jsb.2006.07.014, 16973379
    • Winkler H. 3D reconstruction and processing of volumetric data incryo-electron tomography. Journal of structural biology 2007, 157(1):126-137. 10.1016/j.jsb.2006.07.014, 16973379.
    • (2007) Journal of structural biology , vol.157 , Issue.1 , pp. 126-137
    • Winkler, H.1
  • 20
    • 79960900012 scopus 로고    scopus 로고
    • Clustering and variance mapsfor cryo-electron tomography using wedge-masked differences
    • 10.1016/j.jsb.2011.05.011, 3150390, 21616153
    • Heumann JM, Hoenger A, Mastronarde DN. Clustering and variance mapsfor cryo-electron tomography using wedge-masked differences. Journal of structural biology 2011, 175(3):288-299. 10.1016/j.jsb.2011.05.011, 3150390, 21616153.
    • (2011) Journal of structural biology , vol.175 , Issue.3 , pp. 288-299
    • Heumann, J.M.1    Hoenger, A.2    Mastronarde, D.N.3
  • 21
    • 71049139404 scopus 로고    scopus 로고
    • Averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization
    • 10.1016/j.str.2009.10.009, 2940245, 20004160
    • Scheres SH, Melero R, Valle M, Carazo JM. Averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization. Structure 2009, 17(12):1563-1572. 10.1016/j.str.2009.10.009, 2940245, 20004160.
    • (2009) Structure , vol.17 , Issue.12 , pp. 1563-1572
    • Scheres, S.H.1    Melero, R.2    Valle, M.3    Carazo, J.M.4
  • 23
    • 58349085125 scopus 로고    scopus 로고
    • Tomographic subvolume alignment and subvolume classification applied to myosin V and SIV envelope spikes
    • 10.1016/j.jsb.2008.10.004, 2656979, 19032983
    • Winkler H, Zhu P, Liu J, Ye F, Roux KH, Taylor KA. Tomographic subvolume alignment and subvolume classification applied to myosin V and SIV envelope spikes. Journal of structural biology 2009, 165(2):64-77. 10.1016/j.jsb.2008.10.004, 2656979, 19032983.
    • (2009) Journal of structural biology , vol.165 , Issue.2 , pp. 64-77
    • Winkler, H.1    Zhu, P.2    Liu, J.3    Ye, F.4    Roux, K.H.5    Taylor, K.A.6
  • 24
    • 77953613557 scopus 로고    scopus 로고
    • Probabilistic principal component analysis with expectation maximization (PPCA-EM) facilitates volume classification and estimates the missing data
    • 10.1016/j.jsb.2010.04.002, 3353830, 20385241
    • Yu L, Snapp RR, Ruiz T, Radermacher M. Probabilistic principal component analysis with expectation maximization (PPCA-EM) facilitates volume classification and estimates the missing data. Journal of structural biology 2010, 171(1):18-30. 10.1016/j.jsb.2010.04.002, 3353830, 20385241.
    • (2010) Journal of structural biology , vol.171 , Issue.1 , pp. 18-30
    • Yu, L.1    Snapp, R.R.2    Ruiz, T.3    Radermacher, M.4
  • 25
    • 79955673732 scopus 로고    scopus 로고
    • Classification of electron sub-tomograms with neural networks and its application to template-matching
    • 10.1016/j.jsb.2011.02.009, 21382496
    • Yu Z, Frangakis AS. Classification of electron sub-tomograms with neural networks and its application to template-matching. Journal of structural biology 2011, 174(3):494-504. 10.1016/j.jsb.2011.02.009, 21382496.
    • (2011) Journal of structural biology , vol.174 , Issue.3 , pp. 494-504
    • Yu, Z.1    Frangakis, A.S.2
  • 26
    • 84860574289 scopus 로고    scopus 로고
    • Dynamo A flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in High-Performance Computing
    • 10.1016/j.jsb.2011.12.017, 22245546
    • Castaño-Díez D, Kudryashev M, Arheit M, Stahlberg H. Dynamo A flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in High-Performance Computing. Journal of structural biology 2012, 178(2):139-151. 10.1016/j.jsb.2011.12.017, 22245546.
    • (2012) Journal of structural biology , vol.178 , Issue.2 , pp. 139-151
    • Castaño-Díez, D.1    Kudryashev, M.2    Arheit, M.3    Stahlberg, H.4
  • 28
    • 34948891095 scopus 로고    scopus 로고
    • Snapshots of nuclear pore complexes in action captured by cryo-electron tomography
    • 10.1038/nature06170, 17851530
    • Beck M, et al. Snapshots of nuclear pore complexes in action captured by cryo-electron tomography. Nature 2007, 449(7162):611-615. 10.1038/nature06170, 17851530.
    • (2007) Nature , vol.449 , Issue.7162 , pp. 611-615
    • Beck, M.1
  • 29
    • 0004076664 scopus 로고
    • Angular momentum
    • Oxford University Press, USA
    • Brink D, Satchler G. Angular momentum. 1993, Oxford University Press, USA.
    • (1993)
    • Brink, D.1    Satchler, G.2
  • 30
    • 0003982971 scopus 로고    scopus 로고
    • Numerical optimization
    • Springer, Berlin
    • Nocedal J, Wright S. Numerical optimization. 2006, Springer, Berlin.
    • (2006)
    • Nocedal, J.1    Wright, S.2
  • 32
    • 84922988267 scopus 로고    scopus 로고
    • Three-dimensional electron microscopy of macromolecular assemblies: visualization of biological molecules in their native state
    • Oxford University Press, USA
    • Frank J. Three-dimensional electron microscopy of macromolecular assemblies: visualization of biological molecules in their native state. 2006, Oxford University Press, USA.
    • (2006)
    • Frank, J.1
  • 33
    • 67650544797 scopus 로고    scopus 로고
    • Detective quantum efficiency of electron area detectors in electron microscopy
    • 10.1016/j.ultramic.2009.04.002, 2864625, 19497671
    • McMullan G, Chen S, Henderson R, Faruqi A. Detective quantum efficiency of electron area detectors in electron microscopy. Ultramicroscopy 2009, 109(9):1126-1143. 10.1016/j.ultramic.2009.04.002, 2864625, 19497671.
    • (2009) Ultramicroscopy , vol.109 , Issue.9 , pp. 1126-1143
    • McMullan, G.1    Chen, S.2    Henderson, R.3    Faruqi, A.4
  • 34
    • 0032780181 scopus 로고    scopus 로고
    • Situs: A Package for Docking Crystal Structures into Low-Resolution Maps from Electron Microscopy
    • 10.1006/jsbi.1998.4080, 10222274
    • Wriggers W, Milligan R, McCammon J. Situs: A Package for Docking Crystal Structures into Low-Resolution Maps from Electron Microscopy. Journal of Structural Biology 1999, 125(2-3):185-195. 10.1006/jsbi.1998.4080, 10222274.
    • (1999) Journal of Structural Biology , vol.125 , Issue.2-3 , pp. 185-195
    • Wriggers, W.1    Milligan, R.2    McCammon, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.