Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps
Tài liệu tham khảo
Baker, 2010, Cryo-EM of macromolecular assemblies at near-atomic resolution, Nat. Protoc., 5, 1697, 10.1038/nprot.2010.126
Bothner, 2005, Maturation of a tetravirus capsid alters the dynamic properties and creates a metastable complex, Virology, 334, 17, 10.1016/j.virol.2005.01.017
Doerschuk, 2000, Ab initio reconstruction and experimental design for cryo electron microscopy, IEEE Trans. Info. Theory, 46, 1714, 10.1109/18.857786
Domitrovic, Tatiana, Matsui, Tsutomu, Johnson, John E., 2012. Dissecting quasi-equivalence in non-enveloped viruses: membrane disruption is promoted by lytic peptides released from subunit pentamers, not hexamers. J. Virol. (VI Accepts, published online ahead of print on 3 July 2012). http://dx.doi.org/10.1128/JVI.01089-12.
EM Data Bank. Available at: <http://www.emdatabank.org/>.
Erickson, 1973, The Fourier transform of an electron micrograph—first order and second order theory of image formation, vol. 5, 163
Fuller, 1996, Three-dimensional reconstruction of icosahedral particles – the uncommon line, J. Struct. Biol., 116, 48, 10.1006/jsbi.1996.0009
Helgstrand, 2004, The refined structure of Nudaurelia capensis ω Virus reveals control elements for a T=4 capsid maturation, Virology, 318, 192, 10.1016/j.virol.2003.08.045
Jensen, Grant J. (Ed.), 2010a. Cryo-EM, Part A: Sample Preparation and Data Collection, Methods in Enzymology, vol. 481. Elsevier Inc.
Jensen, Grant J. (Ed.), 2010b. Cryo-EM, Part B: 3-D Reconstruction, Methods in Enzymology, vol. 482. Elsevier Inc.
Jensen, Grant J. (Ed.), 2010c. Cryo-EM, Part C: Analyses, Interpretation, and Case Studies, Methods in Enzymology, vol. 483. Elsevier Inc.
Lee, 2007, Exact reduced-complexity maximum likelihood reconstruction of multiple 3-D objects from unlabeled unoriented 2-D projections and electron microscopy of viruses, IEEE Trans. Image Proc., 16, 2865, 10.1109/TIP.2007.908298
Lee, 2011, Multi-class maximum likelihood symmetry determination and motif reconstruction of 3-D helical objects from projection images for electron microscopy, IEEE Trans. Image Proc., 20, 1962, 10.1109/TIP.2011.2107329
Lehmann, 1998
Lepault, 1984, Projected structure of unstained, frozen-hydrated T-layer of Bacillus brevis, EMBO J., 3, 101, 10.1002/j.1460-2075.1984.tb01768.x
Liu, 2010, Atomic structure of human adenovirus by cryo-EM reveals interactions among protein networks, Science, 329, 1038, 10.1126/science.1187433
Mathworks. Available at: <http://www.mathworks.com/>.
Matsui, 2010, Subunits fold at position-dependent rates during maturation of a eukaryotic RNA virus, Proc. Natl. Acad. Sci. USA, 107, 14111, 10.1073/pnas.1004221107
Munshi, 1996, The 2.8Å structure of a T=4 animal virus and its implications for membrane translocation of RNA, J. Mol. Biol., 261, 1, 10.1006/jmbi.1996.0437
Octave. Available at: <http://www.gnu.org/software/octave/, http://octave.sourceforge.net/>.
Penczek, 2006, Estimation of variance in single-particle reconstruction using the bootstrap technique, J. Struct. Biol., 154, 168, 10.1016/j.jsb.2006.01.003
Pettersen, 2004, UCSF Chimera—a visualization system for exploratory research and analysis, J. Comput. Chem., 25, 1605, 10.1002/jcc.20084
Provencher, 1988, Three-dimensional reconstructions from electron micrographs of disordered specimens: I. Method, Ultramicroscopy, 25, 209, 10.1016/0304-3991(88)90016-2
Prust, 2009, J. Struct. Biol., 167, 185, 10.1016/j.jsb.2009.04.013
Redner, 1984, Mixture densities, maximum likelihood and the EM algorithm, SIAM Rev., 26, 195, 10.1137/1026034
Scheres, 2010, Classification of structural heterogeneity by maximum-likelihood methods, vol. 482, 295
Scheres, 2012, A Bayesian view on cryo-EM structure determination, J. Mol. Biol., 415, 406, 10.1016/j.jmb.2011.11.010
Scheres, 2007, Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization, Nat. Methods, 4, 27, 10.1038/nmeth992
Sigworth, 1998, A maximum-likelihood approach to single-particle image refinement, J. Struct. Biol., 122, 328, 10.1006/jsbi.1998.4014
Sigworth, 2010, An introduction to maximum-likelihood methods in cryo-EM, vol. 482, 263
Taylor, 2002, Large-scale, pH-dependent, quaternary structure changes in an RNA virus capsid are reversible in the absence of subunit autoproteolysis, J. Virol., 76, 9972, 10.1128/JVI.76.19.9972-9980.2002
Toyoshima, 1988, Contrast transfer for frozen-hydrated specimens: determination from pairs of defocused images, Ultramicroscopy, 25, 279, 10.1016/0304-3991(88)90003-4
VIPERdb. Available at: <http://viperdb.scripps.edu/>.
Vogel, 1988, Three-dimensional reconstructions from electron micrographs of disordered specimens: II. Implementation and results, Ultramicroscopy, 25, 223, 10.1016/0304-3991(88)90017-4
Vogel, 1986, Envelope structure of Semliki Forest virus reconstructed from cryo-electron micrographs, Nature, 320, 533, 10.1038/320533a0
Yin, 2003, A statistical approach to computer processing of cryo electron microscope images: virion classification and 3-D reconstruction, J. Struct. Biol., 144, 24, 10.1016/j.jsb.2003.09.023
Zhang, 2008, Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction, Proc. Natl. Acad. Sci. USA, 105, 1867, 10.1073/pnas.0711623105
Zheng, 2000, Explicit computation of orthonormal symmetrized harmonics with application to the identity representation of the icosahedral group, SIAM J. Math. Anal., 32, 538, 10.1137/S0036141098341770