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Items: 1 to 20 of 193

1.

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.

2.

De Novo modeling in cryo-EM density maps with Pathwalking.

Chen M, Baldwin PR, Ludtke SJ, Baker ML.

J Struct Biol. 2016 Dec;196(3):289-298. doi: 10.1016/j.jsb.2016.06.004. Epub 2016 Jul 17.

3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

8.

Cryo electron microscopy to determine the structure of macromolecular complexes.

Carroni M, Saibil HR.

Methods. 2016 Feb 15;95:78-85. doi: 10.1016/j.ymeth.2015.11.023. Epub 2015 Nov 27. Review.

9.

Cryo-electron microscopy and X-ray crystallography: complementary approaches to structural biology and drug discovery.

Vénien-Bryan C, Li Z, Vuillard L, Boutin JA.

Acta Crystallogr F Struct Biol Commun. 2017 Apr 1;73(Pt 4):174-183. doi: 10.1107/S2053230X17003740. Epub 2017 Mar 29. Review.

PMID:
28368275
10.

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.

11.

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.

12.

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.

13.

How cryo-EM is revolutionizing structural biology.

Bai XC, McMullan G, Scheres SH.

Trends Biochem Sci. 2015 Jan;40(1):49-57. doi: 10.1016/j.tibs.2014.10.005. Epub 2014 Nov 7. Review.

PMID:
25544475
14.

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.

Wang RY, Song Y, Barad BA, Cheng Y, Fraser JS, DiMaio F.

Elife. 2016 Sep 26;5. pii: e17219. doi: 10.7554/eLife.17219.

15.

Refinement of Atomic Structures Against cryo-EM Maps.

Murshudov GN.

Methods Enzymol. 2016;579:277-305. doi: 10.1016/bs.mie.2016.05.033. Epub 2016 Jun 24. Review.

PMID:
27572731
16.

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.

17.

RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps.

Frenz B, Walls AC, Egelman EH, Veesler D, DiMaio F.

Nat Methods. 2017 Aug;14(8):797-800. doi: 10.1038/nmeth.4340. Epub 2017 Jun 19.

PMID:
28628127
18.

Denoising of high-resolution single-particle electron-microscopy density maps by their approximation using three-dimensional Gaussian functions.

Jonić S, Vargas J, Melero R, Gómez-Blanco J, Carazo JM, Sorzano CO.

J Struct Biol. 2016 Jun;194(3):423-33. doi: 10.1016/j.jsb.2016.04.007. Epub 2016 Apr 13.

PMID:
27085420
19.

Sample preparation of biological macromolecular assemblies for the determination of high-resolution structures by cryo-electron microscopy.

Stark H, Chari A.

Microscopy (Oxf). 2016 Feb;65(1):23-34. doi: 10.1093/jmicro/dfv367. Epub 2015 Dec 15. Review.

PMID:
26671943
20.

Cross-validation in cryo-EM-based structural modeling.

Falkner B, Schröder GF.

Proc Natl Acad Sci U S A. 2013 May 28;110(22):8930-5. doi: 10.1073/pnas.1119041110. Epub 2013 May 14.

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