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Items: 1 to 20 of 298

1.

Cryo-EM of macromolecular assemblies at near-atomic resolution.

Baker ML, Zhang J, Ludtke SJ, Chiu W.

Nat Protoc. 2010 Sep;5(10):1697-708. doi: 10.1038/nprot.2010.126. Epub 2010 Sep 30.

2.

Analyses of subnanometer resolution cryo-EM density maps.

Baker ML, Baker MR, Hryc CF, Dimaio F.

Methods Enzymol. 2010;483:1-29. doi: 10.1016/S0076-6879(10)83001-0.

3.

Modeling protein structure at near atomic resolutions with Gorgon.

Baker ML, Abeysinghe SS, Schuh S, Coleman RA, Abrams A, Marsh MP, Hryc CF, Ruths T, Chiu W, Ju T.

J Struct Biol. 2011 May;174(2):360-73. doi: 10.1016/j.jsb.2011.01.015. Epub 2011 Feb 4.

4.

Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps.

Baker ML, Baker MR, Hryc CF, Ju T, Chiu W.

Biopolymers. 2012 Sep;97(9):655-68. doi: 10.1002/bip.22065.

5.

EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies.

Dror O, Lasker K, Nussinov R, Wolfson H.

Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):42-9. Epub 2006 Dec 13.

6.

Constructing and validating initial Cα models from subnanometer resolution density maps with pathwalking.

Baker MR, Rees I, Ludtke SJ, Chiu W, Baker ML.

Structure. 2012 Mar 7;20(3):450-63. doi: 10.1016/j.str.2012.01.008.

7.

Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography.

Trabuco LG, Villa E, Schreiner E, Harrison CB, Schulten K.

Methods. 2009 Oct;49(2):174-80. doi: 10.1016/j.ymeth.2009.04.005. Epub 2009 May 4.

8.

Mechanism of folding chamber closure in a group II chaperonin.

Zhang J, Baker ML, Schröder GF, Douglas NR, Reissmann S, Jakana J, Dougherty M, Fu CJ, Levitt M, Ludtke SJ, Frydman J, Chiu W.

Nature. 2010 Jan 21;463(7279):379-83. doi: 10.1038/nature08701.

9.

FOLD-EM: automated fold recognition in medium- and low-resolution (4-15 Å) electron density maps.

Saha M, Morais MC.

Bioinformatics. 2012 Dec 15;28(24):3265-73. doi: 10.1093/bioinformatics/bts616. Epub 2012 Nov 6.

10.

Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction.

Zhang X, Settembre E, Xu C, Dormitzer PR, Bellamy R, Harrison SC, Grigorieff N.

Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):1867-72. doi: 10.1073/pnas.0711623105. Epub 2008 Jan 31.

11.

Cryogenic electron microscopy and single-particle analysis.

Elmlund D, Elmlund H.

Annu Rev Biochem. 2015;84:499-517. doi: 10.1146/annurev-biochem-060614-034226. Epub 2015 Feb 26. Review.

PMID:
25747402
12.

Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions.

Brown A, Long F, Nicholls RA, Toots J, Emsley P, Murshudov G.

Acta Crystallogr D Biol Crystallogr. 2015 Jan 1;71(Pt 1):136-53. doi: 10.1107/S1399004714021683. Epub 2015 Jan 1.

13.

EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps.

Lindert S, Alexander N, Wötzel N, Karakaş M, Stewart PL, Meiler J.

Structure. 2012 Mar 7;20(3):464-78. doi: 10.1016/j.str.2012.01.023.

14.

Structure of HIV-1 capsid assemblies by cryo-electron microscopy and iterative helical real-space reconstruction.

Meng X, Zhao G, Zhang P.

J Vis Exp. 2011 Aug 9;(54). pii: 3041. doi: 10.3791/3041.

15.

Seeing GroEL at 6 A resolution by single particle electron cryomicroscopy.

Ludtke SJ, Chen DH, Song JL, Chuang DT, Chiu W.

Structure. 2004 Jul;12(7):1129-36.

16.

A primer to single-particle cryo-electron microscopy.

Cheng Y, Grigorieff N, Penczek PA, Walz T.

Cell. 2015 Apr 23;161(3):438-49. doi: 10.1016/j.cell.2015.03.050. Review.

17.

Conventional electron microscopy, cryo-electron microscopy and cryo-electron tomography of viruses.

Castón JR.

Subcell Biochem. 2013;68:79-115. doi: 10.1007/978-94-007-6552-8_3. Review.

PMID:
23737049
18.

Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement.

Zhu J, Cheng L, Fang Q, Zhou ZH, Honig B.

J Mol Biol. 2010 Apr 2;397(3):835-51. doi: 10.1016/j.jmb.2010.01.041. Epub 2010 Jan 28.

19.

Cryo-electron microscopy--a primer for the non-microscopist.

Milne JL, Borgnia MJ, Bartesaghi A, Tran EE, Earl LA, Schauder DM, Lengyel J, Pierson J, Patwardhan A, Subramaniam S.

FEBS J. 2013 Jan;280(1):28-45. doi: 10.1111/febs.12078. Epub 2012 Dec 17. Review.

20.

Single particle cryo-electron microscopy and 3-D reconstruction of viruses.

Guo F, Jiang W.

Methods Mol Biol. 2014;1117:401-43. doi: 10.1007/978-1-62703-776-1_19.

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