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Volumn 198, Issue 2, 2017, Pages 124-133

Focus: The interface between data collection and data processing in cryo-EM

Author keywords

Automated data collection; Cryo EM; Drift correction; High throughput image processing

Indexed keywords

ARTICLE; COMPUTER INTERFACE; CRYOELECTRON MICROSCOPY; DATA ANALYSIS; DATA EXTRACTION; DATA SYNTHESIS; IMAGE PROCESSING; IMAGING SOFTWARE; INFORMATION PROCESSING; PRIORITY JOURNAL; AUTOMATION; PROCEDURES; SIGNAL NOISE RATIO; SOFTWARE;

EID: 85018192388     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2017.03.007     Document Type: Article
Times cited : (163)

References (44)
  • 1
    • 84860574289 scopus 로고    scopus 로고
    • Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments
    • 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 environments. J. Struct. Biol. 178 (2012), 139–151.
    • (2012) J. Struct. Biol. , vol.178 , pp. 139-151
    • Castaño-Díez, D.1    Kudryashev, M.2    Arheit, M.3    Stahlberg, H.4
  • 5
    • 84891016898 scopus 로고    scopus 로고
    • SPRING – An image processing package for single-particle based helical reconstruction from electron cryomicrographs
    • Desfosses, A., Ciuffa, R., Gutsche, I., Sachse, C., SPRING – An image processing package for single-particle based helical reconstruction from electron cryomicrographs. J. Struct. Biol. 185 (2014), 15–26.
    • (2014) J. Struct. Biol. , vol.185 , pp. 15-26
    • Desfosses, A.1    Ciuffa, R.2    Gutsche, I.3    Sachse, C.4
  • 6
    • 33845305513 scopus 로고    scopus 로고
    • The iterative helical real space reconstruction method: surmounting the problems posed by real polymers
    • Egelman, E.H., The iterative helical real space reconstruction method: surmounting the problems posed by real polymers. J. Struct. Biol. 157 (2007), 83–94.
    • (2007) J. Struct. Biol. , vol.157 , pp. 83-94
    • Egelman, E.H.1
  • 7
    • 85013142118 scopus 로고    scopus 로고
    • A pipeline approach to single-particle processing in RELION
    • Fernandez-Leiro, R., Scheres, S., A pipeline approach to single-particle processing in RELION. bioRXiv, 2016, 10.1101/078352.
    • (2016) bioRXiv
    • Fernandez-Leiro, R.1    Scheres, S.2
  • 8
    • 36049000626 scopus 로고    scopus 로고
    • 2dx_merge: data management and merging for 2D crystal images
    • Gipson, B., Zeng, X., Stahlberg, H., 2dx_merge: data management and merging for 2D crystal images. J. Struct. Biol. 160 (2007), 375–384.
    • (2007) J. Struct. Biol. , vol.160 , pp. 375-384
    • Gipson, B.1    Zeng, X.2    Stahlberg, H.3
  • 9
    • 33845330614 scopus 로고    scopus 로고
    • 2dx – user-friendly image processing for 2D crystals
    • Gipson, B., Zeng, X., Zhang, Z.Y., Stahlberg, H., 2dx – user-friendly image processing for 2D crystals. J. Struct. Biol. 157 (2007), 64–72.
    • (2007) J. Struct. Biol. , vol.157 , pp. 64-72
    • Gipson, B.1    Zeng, X.2    Zhang, Z.Y.3    Stahlberg, H.4
  • 10
    • 28444450878 scopus 로고    scopus 로고
    • Lipid-protein interactions in double-layered two-dimensional AQP0 crystals
    • Gonen, T., Cheng, Y., Sliz, P., Hiroaki, Y., Fujiyoshi, Y., Harrison, S.C., Walz, T., Lipid-protein interactions in double-layered two-dimensional AQP0 crystals. Nature 438 (2005), 633–638.
    • (2005) Nature , vol.438 , pp. 633-638
    • Gonen, T.1    Cheng, Y.2    Sliz, P.3    Hiroaki, Y.4    Fujiyoshi, Y.5    Harrison, S.C.6    Walz, T.7
  • 11
    • 84930634509 scopus 로고    scopus 로고
    • Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6
    • Grant, T., Grigorieff, N., Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6. Elife, 4, 2015, e06980.
    • (2015) Elife , vol.4 , pp. e06980
    • Grant, T.1    Grigorieff, N.2
  • 12
    • 33845348200 scopus 로고    scopus 로고
    • FREALIGN: high-resolution refinement of single particle structures
    • Grigorieff, N., FREALIGN: high-resolution refinement of single particle structures. J. Struct. Biol. 157 (2007), 117–125.
    • (2007) J. Struct. Biol. , vol.157 , pp. 117-125
    • Grigorieff, N.1
  • 13
    • 84974849211 scopus 로고    scopus 로고
    • Frealign: An exploratory tool for single-particle cryo-EM
    • Grigorieff, N., Frealign: An exploratory tool for single-particle cryo-EM. Methods Enzymol. 579 (2016), 191–226.
    • (2016) Methods Enzymol. , vol.579 , pp. 191-226
    • Grigorieff, N.1
  • 14
    • 85006371642 scopus 로고    scopus 로고
    • Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging
    • Hagen, W.J., Wan, W., Briggs, J.A., Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging. J. Struct. Biol. 197:2 (2016), 191–198.
    • (2016) J. Struct. Biol. , vol.197 , Issue.2 , pp. 191-198
    • Hagen, W.J.1    Wan, W.2    Briggs, J.A.3
  • 16
    • 0029879295 scopus 로고    scopus 로고
    • Computer visualization of three-dimensional image data using IMOD
    • Kremer, J.R., Mastronarde, D.N., McIntosh, J.R., Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116 (1996), 71–76.
    • (1996) J. Struct. Biol. , vol.116 , pp. 71-76
    • Kremer, J.R.1    Mastronarde, D.N.2    McIntosh, J.R.3
  • 17
    • 84897000286 scopus 로고    scopus 로고
    • The resolution revolution
    • Kühlbrandt, W., The resolution revolution. Science 343 (2014), 1443–1444.
    • (2014) Science , vol.343 , pp. 1443-1444
    • Kühlbrandt, W.1
  • 20
    • 84880848354 scopus 로고    scopus 로고
    • Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM
    • Li, X., Mooney, P., Zheng, S., Booth, C.R., Braunfeld, M.B., Gubbens, S., Agard, D.A., Cheng, Y., Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods 10 (2013), 584–590.
    • (2013) Nat. Methods , vol.10 , pp. 584-590
    • Li, X.1    Mooney, P.2    Zheng, S.3    Booth, C.R.4    Braunfeld, M.B.5    Gubbens, S.6    Agard, D.A.7    Cheng, Y.8
  • 21
    • 84946482375 scopus 로고    scopus 로고
    • Asynchronous data acquisition and on-the-fly analysis of dose fractionated cryoEM images by UCSFImage
    • Li, X., Zheng, S., Agard, D.A., Cheng, Y., Asynchronous data acquisition and on-the-fly analysis of dose fractionated cryoEM images by UCSFImage. J. Struct. Biol. 192 (2015), 174–178.
    • (2015) J. Struct. Biol. , vol.192 , pp. 174-178
    • Li, X.1    Zheng, S.2    Agard, D.A.3    Cheng, Y.4
  • 22
    • 85013784291 scopus 로고    scopus 로고
    • Single-particle refinement and variability analysis in EMAN2.1
    • Ludtke, S.J., Single-particle refinement and variability analysis in EMAN2.1. Methods Enzymol. 579 (2016), 159–189.
    • (2016) Methods Enzymol. , vol.579 , pp. 159-189
    • Ludtke, S.J.1
  • 23
    • 84883447961 scopus 로고    scopus 로고
    • Likelihood-based classification of cryo-EM images using FREALIGN
    • Lyumkis, D., Brilot, A.F., Theobald, D.L., Grigorieff, N., Likelihood-based classification of cryo-EM images using FREALIGN. J. Struct. Biol. 183 (2013), 377–388.
    • (2013) J. Struct. Biol. , vol.183 , pp. 377-388
    • Lyumkis, D.1    Brilot, A.F.2    Theobald, D.L.3    Grigorieff, N.4
  • 24
    • 25644458666 scopus 로고    scopus 로고
    • Automated electron microscope tomography using robust prediction of specimen movements
    • Mastronarde, D.N., Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152 (2005), 36–51.
    • (2005) J. Struct. Biol. , vol.152 , pp. 36-51
    • Mastronarde, D.N.1
  • 25
    • 85019315346 scopus 로고    scopus 로고
    • Robust image alignment for cryogenic transmission electron microscopy
    • McLeod, R.A., Kowal, J., Ringler, P., Stahlberg, H., Robust image alignment for cryogenic transmission electron microscopy. J. Struct. Biol. 179:3 (2016), 179–293.
    • (2016) J. Struct. Biol. , vol.179 , Issue.3 , pp. 179-293
    • McLeod, R.A.1    Kowal, J.2    Ringler, P.3    Stahlberg, H.4
  • 29
    • 84945967753 scopus 로고    scopus 로고
    • Automated batch fiducial-less tilt-series alignment in Appion using Protomo
    • Noble, A.J., Stagg, S.M., Automated batch fiducial-less tilt-series alignment in Appion using Protomo. J. Struct. Biol. 192 (2015), 270–278.
    • (2015) J. Struct. Biol. , vol.192 , pp. 270-278
    • Noble, A.J.1    Stagg, S.M.2
  • 30
    • 85011645437 scopus 로고    scopus 로고
    • CryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
    • Punjani, A., Rubinstein, J.L., Fleet, D.J., Brubaker, M.A., CryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14:3 (2017), 290–296.
    • (2017) Nat. Methods , vol.14 , Issue.3 , pp. 290-296
    • Punjani, A.1    Rubinstein, J.L.2    Fleet, D.J.3    Brubaker, M.A.4
  • 31
    • 84963958060 scopus 로고    scopus 로고
    • Methods to account for movement and flexibility in cryo-EM data processing
    • Rawson, S., Iadanza, M.G., Ranson, N.A., Muench, S.P., Methods to account for movement and flexibility in cryo-EM data processing. Methods 100 (2016), 35–41.
    • (2016) Methods , vol.100 , pp. 35-41
    • Rawson, S.1    Iadanza, M.G.2    Ranson, N.A.3    Muench, S.P.4
  • 32
    • 84946488108 scopus 로고    scopus 로고
    • CTFFIND4: Fast and accurate defocus estimation from electron micrographs
    • Rohou, A., Grigorieff, N., CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192:2 (2015), 216–221.
    • (2015) J. Struct. Biol. , vol.192 , Issue.2 , pp. 216-221
    • Rohou, A.1    Grigorieff, N.2
  • 33
    • 84946473054 scopus 로고    scopus 로고
    • Alignment of cryo-EM movies of individual particles by optimization of image translations
    • Rubinstein, J.L., Brubaker, M.A., Alignment of cryo-EM movies of individual particles by optimization of image translations. J. Struct. Biol. 192 (2015), 188–195.
    • (2015) J. Struct. Biol. , vol.192 , pp. 188-195
    • Rubinstein, J.L.1    Brubaker, M.A.2
  • 34
    • 84888064039 scopus 로고    scopus 로고
    • Quantitative characterization of electron detectors for transmission electron microscopy
    • Ruskin, R.S., Yu, Z., Grigorieff, N., Quantitative characterization of electron detectors for transmission electron microscopy. J. Struct. Biol. 184 (2013), 385–393.
    • (2013) J. Struct. Biol. , vol.184 , pp. 385-393
    • Ruskin, R.S.1    Yu, Z.2    Grigorieff, N.3
  • 35
    • 84899967993 scopus 로고    scopus 로고
    • 2dx_automator: implementation of a semiautomatic high-throughput high-resolution cryo-electron crystallography pipeline
    • Scherer, S., Kowal, J., Chami, M., Dandey, V., Arheit, M., Ringler, P., Stahlberg, H., 2dx_automator: implementation of a semiautomatic high-throughput high-resolution cryo-electron crystallography pipeline. J. Struct. Biol. 186 (2014), 302–307.
    • (2014) J. Struct. Biol. , vol.186 , pp. 302-307
    • Scherer, S.1    Kowal, J.2    Chami, M.3    Dandey, V.4    Arheit, M.5    Ringler, P.6    Stahlberg, H.7
  • 36
    • 84868444740 scopus 로고    scopus 로고
    • RELION: implementation of a Bayesian approach to cryo-EM structure determination
    • Scheres, S.H.W., RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180 (2012), 519–530.
    • (2012) J. Struct. Biol. , vol.180 , pp. 519-530
    • Scheres, S.H.W.1
  • 37
    • 0031704540 scopus 로고    scopus 로고
    • A maximum-likelihood approach to single-particle image refinement
    • Sigworth, F.J., A maximum-likelihood approach to single-particle image refinement. J. Struct. Biol. 122 (1998), 328–339.
    • (1998) J. Struct. Biol. , vol.122 , pp. 328-339
    • Sigworth, F.J.1
  • 41
    • 84994043905 scopus 로고    scopus 로고
    • Antibody-based affinity cryoelectron microscopy at 2.6-Å resolution
    • Yu, G., Li, K., Huang, P., Jiang, X., Jiang, W., Antibody-based affinity cryoelectron microscopy at 2.6-Å resolution. Structure 24 (2016), 1984–1990.
    • (2016) Structure , vol.24 , pp. 1984-1990
    • Yu, G.1    Li, K.2    Huang, P.3    Jiang, X.4    Jiang, W.5
  • 42
    • 84955216953 scopus 로고    scopus 로고
    • Gctf: Real-time CTF determination and correction
    • Zhang, K., Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193 (2016), 1–12.
    • (2016) J. Struct. Biol. , vol.193 , pp. 1-12
    • Zhang, K.1
  • 43
    • 85014129582 scopus 로고    scopus 로고
    • MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy
    • Zheng, S.Q., Palovcak, E., Armache, J.-P., Verba, K.A., Cheng, Y., Agard, D.A., MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Meth. 14:4 (2017), 331–332.
    • (2017) Nat. Meth. , vol.14 , Issue.4 , pp. 331-332
    • Zheng, S.Q.1    Palovcak, E.2    Armache, J.-P.3    Verba, K.A.4    Cheng, Y.5    Agard, D.A.6
  • 44
    • 33845319257 scopus 로고    scopus 로고
    • UCSF tomography: an integrated software suite for real-time electron microscopic tomographic data collection, alignment, and reconstruction
    • Zheng, S.Q., Keszthelyi, B., Branlund, E., Lyle, J.M., Braunfeld, M.B., Sedat, J.W., Agard, D.A., UCSF tomography: an integrated software suite for real-time electron microscopic tomographic data collection, alignment, and reconstruction. J. Struct. Biol. 157 (2007), 138–147.
    • (2007) J. Struct. Biol. , vol.157 , pp. 138-147
    • Zheng, S.Q.1    Keszthelyi, B.2    Branlund, E.3    Lyle, J.M.4    Braunfeld, M.B.5    Sedat, J.W.6    Agard, D.A.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.