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Volumn 188, Issue 2, 2014, Pages 134-141

Hybrid electron microscopy normal mode analysis graphical interface and protocol

Author keywords

Continuous conformational changes; Dynamics; Normal mode analysis; Single particle analysis; Software; Structure

Indexed keywords

ARTICLE; CONFORMATIONAL TRANSITION; ELECTRON MICROSCOPY; HYBRID ELECTRON MICROSCOPY NORMAL MODE ANALYSIS; IMAGE ANALYSIS; PRIORITY JOURNAL; STRUCTURE ANALYSIS; ALGORITHM; CHEMISTRY; COMPUTER INTERFACE; COMPUTER PROGRAM; IMAGE PROCESSING; MACROMOLECULE; PROCEDURES; THREE DIMENSIONAL IMAGING;

EID: 84927636805     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2014.09.005     Document Type: Article
Times cited : (20)

References (39)
  • 1
    • 19444379764 scopus 로고    scopus 로고
    • CONDOR, a new parallel, constrained extension of Powell's UOBYQA algorithm: experimental results and comparison with the DFO algorithm
    • Berghen F.V., Bersini H. CONDOR, a new parallel, constrained extension of Powell's UOBYQA algorithm: experimental results and comparison with the DFO algorithm. J. Comput. Appl. Math. 2005, 181:157-175.
    • (2005) J. Comput. Appl. Math. , vol.181 , pp. 157-175
    • Berghen, F.V.1    Bersini, H.2
  • 2
    • 0000216012 scopus 로고
    • Collective protein dynamics and nuclear spin relaxation
    • Bruschweiler R. Collective protein dynamics and nuclear spin relaxation. J. Chem. Phys. 1995, 102:3396-3403.
    • (1995) J. Chem. Phys. , vol.102 , pp. 3396-3403
    • Bruschweiler, R.1
  • 3
    • 0037436340 scopus 로고    scopus 로고
    • Mega-Dalton biomolecular motion captured from electron microscopy reconstructions
    • Chacon P., Tama F., Wriggers W. Mega-Dalton biomolecular motion captured from electron microscopy reconstructions. J. Mol. Biol. 2003, 326:485-492.
    • (2003) J. Mol. Biol. , vol.326 , pp. 485-492
    • Chacon, P.1    Tama, F.2    Wriggers, W.3
  • 5
    • 2342518038 scopus 로고    scopus 로고
    • On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models
    • Delarue M., Dumas P. On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:6957-6962.
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 6957-6962
    • Delarue, M.1    Dumas, P.2
  • 6
    • 0028454915 scopus 로고
    • A new approach for determining low-frequency normal modes in macromolecules
    • Durand P., Trinquier G., Sanejouand Y.H. A new approach for determining low-frequency normal modes in macromolecules. Biopolymers 1994, 34:759-771.
    • (1994) Biopolymers , vol.34 , pp. 759-771
    • Durand, P.1    Trinquier, G.2    Sanejouand, Y.H.3
  • 8
    • 41649087227 scopus 로고    scopus 로고
    • Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections
    • Elad N., Clare D.K., Saibil H.R., Orlova E.V. Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections. J. Struct. Biol. 2008, 162:108-120.
    • (2008) J. Struct. Biol. , vol.162 , pp. 108-120
    • Elad, N.1    Clare, D.K.2    Saibil, H.R.3    Orlova, E.V.4
  • 9
    • 33845340157 scopus 로고    scopus 로고
    • Unsupervised classification of single particles by cluster tracking in multi-dimensional space
    • Fu J., Gao H., Frank J. Unsupervised classification of single particles by cluster tracking in multi-dimensional space. J. Struct. Biol. 2007, 157:226-239.
    • (2007) J. Struct. Biol. , vol.157 , pp. 226-239
    • Fu, J.1    Gao, H.2    Frank, J.3
  • 10
    • 79953216748 scopus 로고    scopus 로고
    • Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation
    • Fu J., Munro J.B., Blanchard S.C., Frank J. Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:4817-4821.
    • (2011) Proc. Natl. Acad. Sci. U.S.A. , vol.108 , pp. 4817-4821
    • Fu, J.1    Munro, J.B.2    Blanchard, S.C.3    Frank, J.4
  • 12
    • 33644838451 scopus 로고    scopus 로고
    • Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues
    • Grob P., Cruse M.J., Inouye C., Peris M., Penczek P.A., Tjian R., Nogales E. Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues. Structure 2006, 14:511-520.
    • (2006) Structure , vol.14 , pp. 511-520
    • Grob, P.1    Cruse, M.J.2    Inouye, C.3    Peris, M.4    Penczek, P.A.5    Tjian, R.6    Nogales, E.7
  • 14
    • 0029878720 scopus 로고    scopus 로고
    • VMD: visual molecular dynamics
    • Humphrey W., Dalke A., Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 1996, 14(33-38):27-38.
    • (1996) J. Mol. Graph. , vol.14 , Issue.33-38 , pp. 27-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 16
    • 18844424991 scopus 로고    scopus 로고
    • Spline-based image-to-volume registration for three-dimensional electron microscopy
    • Jonic S., Sorzano C.O., Thevenaz P., El-Bez C., De Carlo S., Unser M. Spline-based image-to-volume registration for three-dimensional electron microscopy. Ultramicroscopy 2005, 103:303-317.
    • (2005) Ultramicroscopy , vol.103 , pp. 303-317
    • Jonic, S.1    Sorzano, C.O.2    Thevenaz, P.3    El-Bez, C.4    De Carlo, S.5    Unser, M.6
  • 17
    • 84927658291 scopus 로고    scopus 로고
    • ARPACK Users' Guide Society for Industrial and Applied Mathematics.
    • Lehoucq, R., Sorensen, D., Yang, C., 1998. ARPACK Users' Guide Society for Industrial and Applied Mathematics.
    • (1998)
    • Lehoucq, R.1    Sorensen, D.2    Yang, C.3
  • 19
    • 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., Spahn C.M. A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation. J. Struct. Biol. 2006, 154:184-194.
    • (2006) J. Struct. Biol. , vol.154 , pp. 184-194
    • Penczek, P.A.1    Frank, J.2    Spahn, C.M.3
  • 21
    • 0041711007 scopus 로고    scopus 로고
    • UOBYQA: unconstrained optimization by quadratic approximation
    • Powell M.J.D. UOBYQA: unconstrained optimization by quadratic approximation. Math. Program. 2002, 92:555-582.
    • (2002) Math. Program. , vol.92 , pp. 555-582
    • Powell, M.J.D.1
  • 22
    • 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
  • 28
    • 69249187438 scopus 로고    scopus 로고
    • Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion
    • Stember J.N., Wriggers W. Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion. J. Chem. Phys. 2009, 131:074112.
    • (2009) J. Chem. Phys. , vol.131 , pp. 074112
    • Stember, J.N.1    Wriggers, W.2
  • 29
    • 33748351384 scopus 로고    scopus 로고
    • NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps
    • Suhre K., Navaza J., Sanejouand Y.H. NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps. Acta Crystallogr. D Biol. Crystallogr. 2006, 62:1098-1100.
    • (2006) Acta Crystallogr. D Biol. Crystallogr. , vol.62 , pp. 1098-1100
    • Suhre, K.1    Navaza, J.2    Sanejouand, Y.H.3
  • 30
    • 3242875210 scopus 로고    scopus 로고
    • ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement
    • Suhre K., Sanejouand Y.H. ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res. 2004, 32:W610-614.
    • (2004) Nucleic Acids Res. , vol.32 , pp. W610-614
    • Suhre, K.1    Sanejouand, Y.H.2
  • 31
    • 33745024278 scopus 로고    scopus 로고
    • Symmetry, form, and shape: guiding principles for robustness in macromolecular machines
    • Tama F., Brooks C.L. Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Annu. Rev. Biophys. Biomol. Struct. 2006, 35:115-133.
    • (2006) Annu. Rev. Biophys. Biomol. Struct. , vol.35 , pp. 115-133
    • Tama, F.1    Brooks, C.L.2
  • 32
    • 0034308140 scopus 로고    scopus 로고
    • Building-block approach for determining low-frequency normal modes of macromolecules
    • Tama F., Gadea F.X., Marques O., Sanejouand Y.H. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins 2000, 41:1-7.
    • (2000) Proteins , vol.41 , pp. 1-7
    • Tama, F.1    Gadea, F.X.2    Marques, O.3    Sanejouand, Y.H.4
  • 33
    • 1642355235 scopus 로고    scopus 로고
    • Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis
    • Tama F., Miyashita O., Brooks C.L. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J. Mol. Biol. 2004, 337:985-999.
    • (2004) J. Mol. Biol. , vol.337 , pp. 985-999
    • Tama, F.1    Miyashita, O.2    Brooks, C.L.3
  • 34
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Tama F., Sanejouand Y.H. Conformational change of proteins arising from normal mode calculations. Protein Eng. 2001, 14:1-6.
    • (2001) Protein Eng. , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 35
    • 0036382958 scopus 로고    scopus 로고
    • Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory
    • Tama F., Wriggers W., Brooks C.L. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J. Mol. Biol. 2002, 321:297-305.
    • (2002) J. Mol. Biol. , vol.321 , pp. 297-305
    • Tama, F.1    Wriggers, W.2    Brooks, C.L.3
  • 38
    • 4344685227 scopus 로고    scopus 로고
    • Global ribosome motions revealed with elastic network model
    • Wang Y., Rader A.J., Bahar I., Jernigan R.L. Global ribosome motions revealed with elastic network model. J. Struct. Biol. 2004, 147:302-314.
    • (2004) J. Struct. Biol. , vol.147 , pp. 302-314
    • Wang, Y.1    Rader, A.J.2    Bahar, I.3    Jernigan, R.L.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.