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Items: 1 to 20 of 84

1.

Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly.

Lasker K, Topf M, Sali A, Wolfson HJ.

J Mol Biol. 2009 Apr 24;388(1):180-94. doi: 10.1016/j.jmb.2009.02.031. Epub 2009 Feb 20.

2.

Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy.

Topf M, Baker ML, John B, Chiu W, Sali A.

J Struct Biol. 2005 Feb;149(2):191-203.

PMID:
15681235
3.

A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps.

Zhang S, Vasishtan D, Xu M, Topf M, Alber F.

Bioinformatics. 2010 Jun 15;26(12):i261-8. doi: 10.1093/bioinformatics/btq201.

4.

Refinement of protein structures by iterative comparative modeling and CryoEM density fitting.

Topf M, Baker ML, Marti-Renom MA, Chiu W, Sali A.

J Mol Biol. 2006 Apr 14;357(5):1655-68. Epub 2006 Feb 2.

PMID:
16490207
5.

BCL::EM-Fit: rigid body fitting of atomic structures into density maps using geometric hashing and real space refinement.

Woetzel N, Lindert S, Stewart PL, Meiler J.

J Struct Biol. 2011 Sep;175(3):264-76. doi: 10.1016/j.jsb.2011.04.016. Epub 2011 May 4.

6.

Scoring functions for cryoEM density fitting.

Vasishtan D, Topf M.

J Struct Biol. 2011 May;174(2):333-43. doi: 10.1016/j.jsb.2011.01.012. Epub 2011 Feb 4.

PMID:
21296161
7.

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.

8.

Determining macromolecular assembly structures by molecular docking and fitting into an electron density map.

Lasker K, Sali A, Wolfson HJ.

Proteins. 2010 Nov 15;78(15):3205-11. doi: 10.1002/prot.22845.

9.

Protein structure fitting and refinement guided by cryo-EM density.

Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A.

Structure. 2008 Feb;16(2):295-307. doi: 10.1016/j.str.2007.11.016.

10.

Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density.

Baker ML, Jiang W, Wedemeyer WJ, Rixon FJ, Baker D, Chiu W.

PLoS Comput Biol. 2006 Oct 27;2(10):e146. Epub 2006 Sep 27.

11.

ATTRACT-EM: a new method for the computational assembly of large molecular machines using cryo-EM maps.

de Vries SJ, Zacharias M.

PLoS One. 2012;7(12):e49733. doi: 10.1371/journal.pone.0049733. Epub 2012 Dec 14.

12.

Macromolecular assembly structures by comparative modeling and electron microscopy.

Lasker K, Velázquez-Muriel JA, Webb BM, Yang Z, Ferrin TE, Sali A.

Methods Mol Biol. 2012;857:331-50. doi: 10.1007/978-1-61779-588-6_15.

PMID:
22323229
13.

Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.

DiMaio F, Chiu W.

Methods Enzymol. 2016;579:255-76. doi: 10.1016/bs.mie.2016.06.003. Epub 2016 Aug 12. Review.

14.

MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map.

Tjioe E, Lasker K, Webb B, Wolfson HJ, Sali A.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W167-70. doi: 10.1093/nar/gkr490.

15.

Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage.

Pintilie G, Chen DH, Haase-Pettingell CA, King JA, Chiu W.

Biophys J. 2016 Feb 23;110(4):827-39. doi: 10.1016/j.bpj.2015.11.3522. Epub 2015 Dec 30.

16.

Finding rigid bodies in protein structures: Application to flexible fitting into cryoEM maps.

Pandurangan AP, Topf M.

J Struct Biol. 2012 Feb;177(2):520-31. doi: 10.1016/j.jsb.2011.10.011. Epub 2011 Nov 7.

PMID:
22079400
17.

A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy.

Wu X, Milne JL, Borgnia MJ, Rostapshov AV, Subramaniam S, Brooks BR.

J Struct Biol. 2003 Jan;141(1):63-76.

PMID:
12576021
18.

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.

19.

Computational methods for constructing protein structure models from 3D electron microscopy maps.

Esquivel-Rodríguez J, Kihara D.

J Struct Biol. 2013 Oct;184(1):93-102. doi: 10.1016/j.jsb.2013.06.008. Epub 2013 Jun 21.

20.

Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions.

Rusu M, Birmanns S.

J Struct Biol. 2010 Apr;170(1):164-71. doi: 10.1016/j.jsb.2009.12.028. Epub 2010 Jan 7.

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