메뉴 건너뛰기




Volumn 185, Issue 3, 2014, Pages 267-277

Single particle 3D reconstruction for 2D crystal images of membrane proteins

Author keywords

2dx; Cryo electron crystallography; GPGPU; High performance computing; Membrane proteins; Single particle analysis

Indexed keywords

2DX; CRYO-ELECTRON CRYSTALLOGRAPHY; GPGPU; HIGH PERFORMANCE COMPUTING; MEMBRANE PROTEINS; SINGLE-PARTICLE ANALYSIS;

EID: 84894483344     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2013.12.011     Document Type: Article
Times cited : (14)

References (34)
  • 1
    • 0010951451 scopus 로고
    • Maximum-likelihood estimation of the parameters of a multivariate normal distribution
    • Anderson T.W., Olkin I. Maximum-likelihood estimation of the parameters of a multivariate normal distribution. Linear Algebra Appl. 1985, 70:147-171.
    • (1985) Linear Algebra Appl. , vol.70 , pp. 147-171
    • Anderson, T.W.1    Olkin, I.2
  • 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. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles. eLife 2013, 2:e00461.
    • (2013) eLife , vol.2
    • Bai, X.C.1    Fernandez, I.S.2    McMullan, G.3    Scheres, S.H.4
  • 9
    • 0002806690 scopus 로고    scopus 로고
    • OpenMP: an industry standard API for shared-memory programming
    • Dagum L., Menon R. OpenMP: an industry standard API for shared-memory programming. IEEE Comput. Sci. Eng. 1998, 5:46-55.
    • (1998) IEEE Comput. Sci. Eng. , vol.5 , pp. 46-55
    • Dagum, L.1    Menon, R.2
  • 10
    • 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. 2012, 180:420-427.
    • (2012) J. Struct. Biol. , vol.180 , pp. 420-427
    • Elmlund, D.1    Elmlund, H.2
  • 11
    • 0016677738 scopus 로고
    • Averaging of low exposure electron micrographs of non-periodic objects
    • Frank J. Averaging of low exposure electron micrographs of non-periodic objects. Ultramicroscopy 1975, 1:159-162.
    • (1975) Ultramicroscopy , vol.1 , pp. 159-162
    • Frank, J.1
  • 13
    • 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. 2007, 157:117-125.
    • (2007) J. Struct. Biol. , vol.157 , pp. 117-125
    • Grigorieff, N.1
  • 14
    • 0035783171 scopus 로고    scopus 로고
    • Bsoft: image and molecular processing in electron microscopy
    • Heymann J.B. Bsoft: image and molecular processing in electron microscopy. J. Struct. Biol. 2001, 133:156-169.
    • (2001) J. Struct. Biol. , vol.133 , pp. 156-169
    • Heymann, J.B.1
  • 16
    • 33745299232 scopus 로고    scopus 로고
    • Comparing the OpenMP, MPI, and hybrid programming paradigms on an SMP cluster
    • Jost G., Jin H., Mey D., Hatay F.F. Comparing the OpenMP, MPI, and hybrid programming paradigms on an SMP cluster. Proc. EWOMP 2003, 3:2003.
    • (2003) Proc. EWOMP , vol.3 , pp. 2003
    • Jost, G.1    Jin, H.2    Mey, D.3    Hatay, F.F.4
  • 18
    • 0034712851 scopus 로고    scopus 로고
    • The three-dimensional structure of halorhodopsin to 5Å by electron crystallography: a new unbending procedure for two-dimensional crystals by using a global reference structure
    • Kunji E.R., von Gronau S., Oesterhelt D., Henderson R. The three-dimensional structure of halorhodopsin to 5Å by electron crystallography: a new unbending procedure for two-dimensional crystals by using a global reference structure. Proc. Natl. Acad. Sci. USA 2000, 97:4637-4642.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 4637-4642
    • Kunji, E.R.1    von Gronau, S.2    Oesterhelt, D.3    Henderson, R.4
  • 19
    • 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 2013, 10:584-590.
    • (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
  • 20
    • 0033377664 scopus 로고    scopus 로고
    • EMAN: semiautomated software for high-resolution single-particle reconstructions
    • Ludtke S.J., Baldwin P.R., Chiu W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 1999, 128:82-97.
    • (1999) J. Struct. Biol. , vol.128 , pp. 82-97
    • Ludtke, S.J.1    Baldwin, P.R.2    Chiu, W.3
  • 22
    • 0038441501 scopus 로고    scopus 로고
    • Accurate determination of local defocus and specimen tilt in electron microscopy
    • Mindell J.A., Grigorieff N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 2003, 142:334-347.
    • (2003) J. Struct. Biol. , vol.142 , pp. 334-347
    • Mindell, J.A.1    Grigorieff, N.2
  • 23
    • 77957296661 scopus 로고    scopus 로고
    • Resolution measures in molecular electron microscopy
    • Penczek P.A. Resolution measures in molecular electron microscopy. Methods Enzymol. 2010, 482:73-100.
    • (2010) Methods Enzymol. , vol.482 , pp. 73-100
    • Penczek, P.A.1
  • 25
    • 0001339881 scopus 로고
    • Three-dimensional reconstruction of single particles from random and nonrandom tilt series
    • Radermacher M. Three-dimensional reconstruction of single particles from random and nonrandom tilt series. J. Electron Microsc. Tech. 1988, 9:359-394.
    • (1988) J. Electron Microsc. Tech. , vol.9 , pp. 359-394
    • Radermacher, M.1
  • 26
    • 84868444740 scopus 로고    scopus 로고
    • RELION: implementation of a Bayesian approach to cryo-EM structure determination
    • Scheres S.H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 2012, 180:519-530.
    • (2012) J. Struct. Biol. , vol.180 , pp. 519-530
    • Scheres, S.H.1
  • 27
    • 84866078359 scopus 로고    scopus 로고
    • Prevention of overfitting in cryo-EM structure determination
    • Scheres S.H., Chen S. Prevention of overfitting in cryo-EM structure determination. Nat. Methods 2012, 9:853-854.
    • (2012) Nat. Methods , vol.9 , pp. 853-854
    • Scheres, S.H.1    Chen, S.2
  • 28
    • 36749078686 scopus 로고    scopus 로고
    • Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution
    • Schröder G.F., Brunger A.T., Levitt M. Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. Structure 2007, 15:1630-1641.
    • (2007) Structure , vol.15 , pp. 1630-1641
    • Schröder, G.F.1    Brunger, A.T.2    Levitt, M.3
  • 30
    • 8844219659 scopus 로고    scopus 로고
    • Noise bias in the refinement of structures derived from single particles
    • Stewart A., Grigorieff N. Noise bias in the refinement of structures derived from single particles. Ultramicroscopy 2004, 102:67-84.
    • (2004) Ultramicroscopy , vol.102 , pp. 67-84
    • Stewart, A.1    Grigorieff, N.2
  • 32
    • 84876066543 scopus 로고    scopus 로고
    • Evaluation of electron crystallographic data from images of two-dimensional crystals
    • Unger V.M. Evaluation of electron crystallographic data from images of two-dimensional crystals. Methods Mol. Biol. 2013, 955:211-227.
    • (2013) Methods Mol. Biol. , vol.955 , pp. 211-227
    • Unger, V.M.1
  • 33
    • 34548425430 scopus 로고    scopus 로고
    • A maximum likelihood approach to two-dimensional crystals
    • Zeng X., Stahlberg H., Grigorieff N. A maximum likelihood approach to two-dimensional crystals. J. Struct. Biol. 2007, 160:362-374.
    • (2007) J. Struct. Biol. , vol.160 , pp. 362-374
    • Zeng, X.1    Stahlberg, H.2    Grigorieff, N.3
  • 34
    • 79960907297 scopus 로고    scopus 로고
    • Limiting factors in atomic resolution cryo electron microscopy: no simple tricks
    • Zhang X., Zhou Z.H. Limiting factors in atomic resolution cryo electron microscopy: no simple tricks. J. Struct. Biol. 2011, 175:253-263.
    • (2011) J. Struct. Biol. , vol.175 , pp. 253-263
    • Zhang, X.1    Zhou, Z.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.