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Volumn 14, Issue 3, 2017, Pages 290-296

CryoSPARC: Algorithms for rapid unsupervised cryo-EM structure determination

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO CALCULATION; ALGORITHM; ARTICLE; BAYES THEOREM; CALCULATION; CLASSIFICATION; COMPUTER; CRYOELECTRON MICROSCOPY; DENSITY; DNA SEQUENCE; DNA SYNTHESIS; MACROMOLECULE; MICROSCOPE; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN STRUCTURE; SOFTWARE; STOCHASTIC MODEL; ANIMAL; BIOLOGY; CYTOLOGY; ENZYMOLOGY; IMAGE PROCESSING; MOLECULAR MODEL; PLASMODIUM FALCIPARUM; PROCEDURES; RAT; RIBOSOME; THERMUS THERMOPHILUS; THREE DIMENSIONAL IMAGING; ULTRASTRUCTURE;

EID: 85011645437     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.4169     Document Type: Article
Times cited : (4522)

References (50)
  • 1
    • 84897000286 scopus 로고    scopus 로고
    • Biochemistry. the resolution revolution
    • Kühlbrandt, W. Biochemistry. The resolution revolution. Science 343, 1443-1444 (2014).
    • (2014) Science , vol.343 , pp. 1443-1444
    • Kühlbrandt, W.1
  • 2
    • 84905911542 scopus 로고    scopus 로고
    • Structural biology. Beyond blob-ology
    • Smith, M.T.J. & Rubinstein, J.L. Structural biology. Beyond blob-ology. Science 345, 617-619 (2014).
    • (2014) Science , vol.345 , pp. 617-619
    • Smith, M.T.J.1    Rubinstein, J.L.2
  • 3
    • 84889607320 scopus 로고    scopus 로고
    • Structure of the TRPV1 ion channel determined by electron cryo-microscopy
    • Liao, M., Cao, E., Julius, D. & Cheng, Y. Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 504, 107-112 (2013).
    • (2013) Nature , vol.504 , pp. 107-112
    • Liao, M.1    Cao, E.2    Julius, D.3    Cheng, Y.4
  • 4
    • 84878580683 scopus 로고    scopus 로고
    • Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles
    • Bai, X.C., Fernandez, I.S., McMullan, G. & Scheres, S.H.W. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles. eLife 2, e00461 (2013).
    • (2013) ELife , vol.2 , pp. e00461
    • Bai, X.C.1    Fernandez, I.S.2    McMullan, G.3    Scheres, S.H.W.4
  • 5
    • 84942474131 scopus 로고    scopus 로고
    • Structure of a yeast spliceosome at 3.6-angstrom resolution
    • Yan, C. et al. Structure of a yeast spliceosome at 3.6-angstrom resolution. Science 349, 1182-1191 (2015).
    • (2015) Science , vol.349 , pp. 1182-1191
    • Yan, C.1
  • 6
    • 84958883175 scopus 로고    scopus 로고
    • 2.3 Å resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition
    • Banerjee, S. et al. 2.3 Å resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition. Science 351, 871-875 (2016).
    • (2016) Science , vol.351 , pp. 871-875
    • Banerjee, S.1
  • 7
    • 84962427374 scopus 로고    scopus 로고
    • The 3.8 Å resolution cryo-EM structure of Zika virus
    • Sirohi, D. et al. The 3.8 Å resolution cryo-EM structure of Zika virus. Science 352, 467-470 (2016).
    • (2016) Science , vol.352 , pp. 467-470
    • Sirohi, D.1
  • 8
    • 84975221229 scopus 로고    scopus 로고
    • Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome
    • Abeyrathne, P.D., Koh, C.S., Grant, T., Grigorieff, N. & Korostelev, A.A. Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome. eLife 5, e14874 (2016).
    • (2016) ELife , vol.5 , pp. e14874
    • Abeyrathne, P.D.1    Koh, C.S.2    Grant, T.3    Grigorieff, N.4    Korostelev, A.A.5
  • 9
    • 85009208040 scopus 로고    scopus 로고
    • Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2
    • Kimanius, D., Forsberg, B.O., Scheres, S.H. & Lindahl, E. Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. eLife 5, e18722 (2016).
    • (2016) ELife , vol.5 , pp. e18722
    • Kimanius, D.1    Forsberg, B.O.2    Scheres, S.H.3    Lindahl, E.4
  • 10
    • 84887271303 scopus 로고    scopus 로고
    • Avoiding the pitfalls of single particle cryo-electron microscopy: Einstein from noise
    • Henderson, R. Avoiding the pitfalls of single particle cryo-electron microscopy: Einstein from noise. Proc. Natl. Acad. Sci. USA 110, 18037-18041 (2013).
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. 18037-18041
    • Henderson, R.1
  • 11
    • 84863011711 scopus 로고    scopus 로고
    • Outcome of the frst electron microscopy validation task force meeting
    • Henderson, R. et al. Outcome of the frst electron microscopy validation task force meeting. Structure 20, 205-214 (2012).
    • (2012) Structure , vol.20 , pp. 205-214
    • Henderson, R.1
  • 12
    • 84855818650 scopus 로고    scopus 로고
    • A Bayesian view on cryo-EM structure determination
    • Scheres, S.H.W. A Bayesian view on cryo-EM structure determination. J. Mol. Biol. 415, 406-418 (2012).
    • (2012) J. Mol. Biol. , vol.415 , pp. 406-418
    • Scheres, S.H.W.1
  • 13
    • 33845348200 scopus 로고    scopus 로고
    • FREALIGN: High-resolution refnement of single particle structures
    • Grigorieff, N. FREALIGN: high-resolution refnement of single particle structures. J. Struct. Biol. 157, 117-125 (2007).
    • (2007) J. Struct. Biol. , vol.157 , pp. 117-125
    • Grigorieff, N.1
  • 14
    • 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, 1-12 (2016).
    • (2016) J. Struct. Biol. , vol.193 , pp. 1-12
    • Zhang, K.1
  • 15
    • 84895921737 scopus 로고    scopus 로고
    • GEMpicker: A highly parallel GPU-accelerated particle picking tool for cryo-electron microscopy
    • Hoang, T.V., Cavin, X., Schultz, P. & Ritchie, D.W. gEMpicker: a highly parallel GPU-accelerated particle picking tool for cryo-electron microscopy. BMC Struct. Biol. 13, 25 (2013).
    • (2013) BMC Struct. Biol. , vol.13 , pp. 25
    • Hoang, T.V.1    Cavin, X.2    Schultz, P.3    Ritchie, D.W.4
  • 16
    • 0002007506 scopus 로고
    • Progress in digital integrated electronics
    • IEEE
    • Moore, G.E. Progress in digital integrated electronics. In Proc. Int. Elect. Devices Meet 11-13 (IEEE, 1975).
    • (1975) Proc. Int. Elect. Devices Meet , pp. 11-13
    • Moore, G.E.1
  • 17
    • 0031704540 scopus 로고    scopus 로고
    • A maximum-likelihood approach to single-particle image refnement
    • Sigworth, F.J. A maximum-likelihood approach to single-particle image refnement. J. Struct. Biol. 122, 328-339 (1998).
    • (1998) J. Struct. Biol. , vol.122 , pp. 328-339
    • Sigworth, F.J.1
  • 20
    • 84904136037 scopus 로고    scopus 로고
    • Large-scale machine learning with stochastic gradient descent
    • (eds. Lechevallier, Y. & Saporta, G.)
    • Bottou, L. Large-scale machine learning with stochastic gradient descent. In Proc. COMPSTAT'2010 (eds. Lechevallier, Y. & Saporta, G.) 177-186 (2010).
    • (2010) Proc. COMPSTAT'2010 , pp. 177-186
    • Bottou, L.1
  • 23
    • 84962228587 scopus 로고    scopus 로고
    • Models for the a subunits of the Thermus thermophilus V/A-ATPase and Saccharomyces cerevisiae V-ATPase enzymes by cryo-EM and evolutionary covariance
    • Schep, D.G., Zhao, J. & Rubinstein, J.L. Models for the a subunits of the Thermus thermophilus V/A-ATPase and Saccharomyces cerevisiae V-ATPase enzymes by cryo-EM and evolutionary covariance. Proc. Natl. Acad. Sci. USA 113, 3245-3250 (2016).
    • (2016) Proc. Natl. Acad. Sci. USA , vol.113 , pp. 3245-3250
    • Schep, D.G.1    Zhao, J.2    Rubinstein, J.L.3
  • 24
    • 84929335211 scopus 로고    scopus 로고
    • Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase
    • Zhao, J., Benlekbir, S. & Rubinstein, J.L. Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase. Nature 521, 241-245 (2015).
    • (2015) Nature , vol.521 , pp. 241-245
    • Zhao, J.1    Benlekbir, S.2    Rubinstein, J.L.3
  • 27
    • 84898831301 scopus 로고    scopus 로고
    • Go-ICP: Solving 3D registration effciently and Globally optimally
    • (eds. Davis, L. & Hartley, R.) IEEE
    • Yang, J., Li, H. & Jia, Y. Go-ICP: solving 3D registration effciently and Globally optimally. In Proc. IEEE Int. Conf. Comput. Vis. (eds. Davis, L. & Hartley, R.) 1457-1464 (IEEE, 2013).
    • (2013) Proc. IEEE Int. Conf. Comput. Vis , pp. 1457-1464
    • Yang, J.1    Li, H.2    Jia, Y.3
  • 28
    • 84924617498 scopus 로고    scopus 로고
    • 2.8 Å resolution reconstruction of the thermoplasma Acidophilum 20S proteasome using cryo-electron microscopy
    • Campbell, M.G., Veesler, D., Cheng, A., Potter, C.S. & Carragher, B. 2.8 Å resolution reconstruction of the thermoplasma Acidophilum 20S proteasome using cryo-electron microscopy. eLife 4, e06380 (2015).
    • (2015) ELife , vol.4 , pp. e06380
    • Campbell, M.G.1    Veesler, D.2    Cheng, A.3    Potter, C.S.4    Carragher, B.5
  • 29
    • 84905080837 scopus 로고    scopus 로고
    • Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine
    • Wong, W. et al. Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine. eLife 3, 1-20 (2014).
    • (2014) ELife , vol.3 , pp. 1-20
    • Wong, W.1
  • 30
    • 84866078359 scopus 로고    scopus 로고
    • Prevention of overftting in cryo-EM structure determination
    • Scheres, S.H.W. & Chen, S. Prevention of overftting in cryo-EM structure determination. Nat. Methods 9, 853-854 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 853-854
    • Scheres, S.H.W.1    Chen, S.2
  • 31
    • 0142042865 scopus 로고    scopus 로고
    • Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy
    • Rosenthal, P.B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721-745 (2003).
    • (2003) J. Mol. Biol. , vol.333 , pp. 721-745
    • Rosenthal, P.B.1    Henderson, R.2
  • 32
    • 84880607763 scopus 로고    scopus 로고
    • High-resolution noise substitution to measure overftting and validate resolution in 3D structure determination by single particle electron cryomicroscopy
    • Chen, S. et al. High-resolution noise substitution to measure overftting and validate resolution in 3D structure determination by single particle electron cryomicroscopy. Ultramicroscopy 135, 24-35 (2013).
    • (2013) Ultramicroscopy , vol.135 , pp. 24-35
    • Chen, S.1
  • 33
    • 84898599354 scopus 로고    scopus 로고
    • Single particle analysis integrated with microscopy: A high-throughput approach for reconstructing icosahedral particles
    • Yan, X., Cardone, G., Zhang, X., Zhou, Z.H. & Baker, T.S. Single particle analysis integrated with microscopy: a high-throughput approach for reconstructing icosahedral particles. J. Struct. Biol. 186, 8-18 (2014).
    • (2014) J. Struct. Biol. , vol.186 , pp. 8-18
    • Yan, X.1    Cardone, G.2    Zhang, X.3    Zhou, Z.H.4    Baker, T.S.5
  • 34
    • 84878860950 scopus 로고    scopus 로고
    • 3R1 channel
    • 3R1 channel. Structure 21, 900-909 (2013).
    • (2013) Structure , vol.21 , pp. 900-909
    • Murray, S.C.1
  • 35
    • 84985231782 scopus 로고
    • Three-dimensional reconstruction from a single-exposure random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli
    • Radermacher, M., Wagenknecht, T., Verschoor, A. & Frank, J. Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli. J. Microsc. 146, 113-136 (1987).
    • (1987) J. Microsc. , vol.146 , pp. 113-136
    • Radermacher, M.1    Wagenknecht, T.2    Verschoor, A.3    Frank, J.4
  • 36
    • 32544460568 scopus 로고    scopus 로고
    • The orthogonal tilt reconstruction method: An approach to generating single-class volumes with no missing cone for ab initio reconstruction of asymmetric particles
    • Leschziner, A.E. & Nogales, E. The orthogonal tilt reconstruction method: an approach to generating single-class volumes with no missing cone for ab initio reconstruction of asymmetric particles. J. Struct. Biol. 153, 284-299 (2006).
    • (2006) J. Struct. Biol. , vol.153 , pp. 284-299
    • Leschziner, A.E.1    Nogales, E.2
  • 37
    • 84949926366 scopus 로고    scopus 로고
    • Ab initio cryo-EM structure determination as a validation problem
    • (eds. Pesquet-Popescu, B. & Fowler, J.) IEEE
    • Penczek, P.A. & Asturias, F.J. Ab initio cryo-EM structure determination as a validation problem. In Proc. IEEE Int. Conf. on Image Process. (eds. Pesquet-Popescu, B. & Fowler, J.) 2090-2094 (IEEE, 2014).
    • (2014) Proc. IEEE Int. Conf. on Image Process , pp. 2090-2094
    • Penczek, P.A.1    Asturias, F.J.2
  • 38
    • 84923525032 scopus 로고    scopus 로고
    • A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy
    • Sorzano, C.O.S. et al. A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy. J. Struct. Biol. 189, 213-219 (2015).
    • (2015) J. Struct. Biol. , vol.189 , pp. 213-219
    • Sorzano, C.O.S.1
  • 39
    • 77957241724 scopus 로고    scopus 로고
    • A Bayesian method for 3D macromolecular structure inference using class average images from single particle electron microscopy
    • Jaitly, N., Brubaker, M.A., Rubinstein, J.L. & Lilien, R.H. A Bayesian method for 3D macromolecular structure inference using class average images from single particle electron microscopy. Bioinformatics 26, 2406-2415 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 2406-2415
    • Jaitly, N.1    Brubaker, M.A.2    Rubinstein, J.L.3    Lilien, R.H.4
  • 40
    • 84868498215 scopus 로고    scopus 로고
    • SIMPLE: Software for ab initio reconstruction of heterogeneous single-particles
    • Elmlund, D. & Elmlund, H. SIMPLE: Software for ab initio reconstruction of heterogeneous single-particles. J. Struct. Biol. 180, 420-427 (2012).
    • (2012) J. Struct. Biol. , vol.180 , pp. 420-427
    • Elmlund, D.1    Elmlund, H.2
  • 41
    • 84881432897 scopus 로고    scopus 로고
    • PRIME: Probabilistic initial 3D model generation for single-particle cryo-electron microscopy
    • Elmlund, H., Elmlund, D. & Bengio, S. PRIME: probabilistic initial 3D model generation for single-particle cryo-electron microscopy. Structure 21, 1299-1306 (2013).
    • (2013) Structure , vol.21 , pp. 1299-1306
    • Elmlund, H.1    Elmlund, D.2    Bengio, S.3
  • 43
    • 84928695968 scopus 로고    scopus 로고
    • SubspaceEM: A fast maximum-a-posteriori algorithm for cryo-EM single particle reconstruction
    • Dvornek, N.C., Sigworth, F.J. & Tagare, H.D. SubspaceEM: a fast maximum-a-posteriori algorithm for cryo-EM single particle reconstruction. J. Struct. Biol. 190, 200-214 (2015).
    • (2015) J. Struct. Biol. , vol.190 , pp. 200-214
    • Dvornek, N.C.1    Sigworth, F.J.2    Tagare, H.D.3
  • 44
    • 84930661954 scopus 로고    scopus 로고
    • Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud
    • Cianfrocco, M.A. & Leschziner, A.E. Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud. eLife 4, e06664 (2015).
    • (2015) ELife , vol.4 , pp. e06664
    • Cianfrocco, M.A.1    Leschziner, A.E.2
  • 45
    • 84955307962 scopus 로고    scopus 로고
    • Sampling the conformational space of the catalytic subunit of human γ-secretase
    • Bai, X.-C., Rajendra, E., Yang, G., Shi, Y. & Scheres, S.H. Sampling the conformational space of the catalytic subunit of human γ-secretase. eLife 4, e11182 (2015).
    • (2015) ELife , vol.4 , pp. e11182
    • Bai, X.-C.1    Rajendra, E.2    Yang, G.3    Shi, Y.4    Scheres, S.H.5
  • 46
    • 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, 188-195 (2015).
    • (2015) J. Struct. Biol. , vol.192 , pp. 188-195
    • Rubinstein, J.L.1    Brubaker, M.A.2
  • 47
    • 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, e06980 (2015).
    • (2015) ELife , vol.4 , pp. e06980
    • Grant, T.1    Grigorieff, N.2
  • 48
    • 85014378308 scopus 로고    scopus 로고
    • Protocol for rapid unsupervised cryo-EM structure determination using cryoSPARC software
    • Punjani, A., Rubinstein, J., Fleet, D. & Brubaker, M. Protocol for rapid unsupervised cryo-EM structure determination using cryoSPARC software. Protocol Exchange http://dx.doi.org/10.1038/protex.2017.009 (2016).
    • (2016) Protocol Exchange
    • Punjani, A.1    Rubinstein, J.2    Fleet, D.3    Brubaker, M.4
  • 50
    • 84892623436 scopus 로고    scopus 로고
    • On the importance of initialization and momentum in deep learning
    • Sutskever, I., Martens, J., Dahl, G.E. & Hinton, G.E. On the importance of initialization and momentum in deep learning. J. Mach. Learn. Res. 28, 1139-1147 (2013).
    • (2013) J. Mach. Learn. Res. , vol.28 , pp. 1139-1147
    • Sutskever, I.1    Martens, J.2    Dahl, G.E.3    Hinton, G.E.4


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