MPSA related publications

Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm.

Liu X, Jiang W, Jakana J, Chiu W.

J Struct Biol. 2007 Oct;160(1):11-27. Epub 2007 Jul 6.

PMID: 17698370 [PubMed - indexed for MEDLINE] Free PMC Article

Seeing the portal in herpes simplex virus type 1 B capsids.

Rochat RH, Liu X, Murata K, Nagayama K, Rixon FJ, Chiu W.

J Virol. 2011 Feb;85(4):1871-4. doi: 10.1128/JVI.01663-10. Epub 2010 Nov 24.

PMID: 21106752 [PubMed - indexed for MEDLINE] Free PMC Article

Achievable resolution from images of biological specimens acquired from a 4k x 4k CCD camera in a 300-kV electron cryomicroscope.

Chen DH, Jakana J, Liu X, Schmid MF, Chiu W.

J Struct Biol. 2008 Jul;163(1):45-52. doi: 10.1016/j.jsb.2008.04.001. Epub 2008 Apr 14.

PMID: 18514542 [PubMed - indexed for MEDLINE] Free PMC Article

Direct electron detection yields cryo-EM reconstructions at resolutions beyond 3/4 Nyquist frequency.

Bammes BE, Rochat RH, Jakana J, Chen DH, Chiu W.

J Struct Biol. 2012 Mar;177(3):589-601. doi: 10.1016/j.jsb.2012.01.008. Epub 2012 Jan 21.

PMID: 22285189 [PubMed - indexed for MEDLINE] Free PMC Article

Zernike phase contrast cryo-electron microscopy and tomography for structure determination at nanometer and subnanometer resolutions.

Murata K, Liu X, Danev R, Jakana J, Schmid MF, King J, Nagayama K, Chiu W.

Structure. 2010 Aug 11;18(8):903-12. doi: 10.1016/j.str.2010.06.006.

PMID: 20696391 [PubMed - indexed for MEDLINE] Free PMC Article

Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus.

Liu X, Zhang Q, Murata K, Baker ML, Sullivan MB, Fu C, Dougherty MT, Schmid MF, Osburne MS, Chisholm SW, Chiu W.

Nat Struct Mol Biol. 2010 Jul;17(7):830-6. doi: 10.1038/nsmb.1823. Epub 2010 Jun 13.

PMID: 20543830 [PubMed - indexed for MEDLINE] Free PMC Article

Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus.

Chen DH, Baker ML, Hryc CF, DiMaio F, Jakana J, Wu W, Dougherty M, Haase-Pettingell C, Schmid MF, Jiang W, Baker D, King JA, Chiu W.

Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1355-60. doi: 10.1073/pnas.1015739108. Epub 2011 Jan 10.

PMID: 21220301 [PubMed - indexed for MEDLINE] Free PMC Article

The structure of barmah forest virus as revealed by cryo-electron microscopy at a 6-angstrom resolution has detailed transmembrane protein architecture and interactions.

Kostyuchenko VA, Jakana J, Liu X, Haddow AD, Aung M, Weaver SC, Chiu W, Lok SM.

J Virol. 2011 Sep;85(18):9327-33. doi: 10.1128/JVI.05015-11. Epub 2011 Jul 13.

PMID: 21752915 [PubMed - indexed for MEDLINE] Free PMC Article

High-resolution single-particle orientation refinement based on spectrally self-adapting common lines.

Elmlund D, Elmlund H.

J Struct Biol. 2009 Jul;167(1):83-94. doi: 10.1016/j.jsb.2009.04.009. Epub 2009 May 3.

PMID: 19410651 [PubMed - indexed for MEDLINE]

Developing a denoising filter for electron microscopy and tomography data in the cloud.

Starosolski Z, Szczepanski M, Wahle M, Rusu M, Wriggers W.

Biophys Rev. 2012 Sep 1;4(3):223-229.

PMID: 23066432 [PubMed]

The random-model method enables ab initio 3D reconstruction of asymmetric particles and determination of particle symmetry.

Sanz-Garcia E, Stewart AB, Belnap DM.

J Struct Biol. 2010 Aug;171(2):216-22. doi: 10.1016/j.jsb.2010.03.017. Epub 2010 Mar 28.

PMID: 20353825 [PubMed - indexed for MEDLINE] Free PMC Article

Cryo-EM structure of the mature dengue virus at 3.5-Å resolution.

Zhang X, Ge P, Yu X, Brannan JM, Bi G, Zhang Q, Schein S, Zhou ZH.

Nat Struct Mol Biol. 2013 Jan;20(1):105-10. doi: 10.1038/nsmb.2463. Epub 2012 Dec 16.

PMID: 23241927 [PubMed - indexed for MEDLINE] Free PMC Article

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.

PMID: 20885381 [PubMed - indexed for MEDLINE] Free PMC Article

The structure of barmah forest virus as revealed by cryo-electron microscopy at a 6-angstrom resolution has detailed transmembrane protein architecture and interactions.

Kostyuchenko VA, Jakana J, Liu X, Haddow AD, Aung M, Weaver SC, Chiu W, Lok SM.

J Virol. 2011 Sep;85(18):9327-33. doi: 10.1128/JVI.05015-11. Epub 2011 Jul 13.

PMID: 21752915 [PubMed - indexed for MEDLINE] Free PMC Article

JADAS: a customizable automated data acquisition system and its application to ice-embedded single particles.

Zhang J, Nakamura N, Shimizu Y, Liang N, Liu X, Jakana J, Marsh MP, Booth CR, Shinkawa T, Nakata M, Chiu W.

J Struct Biol. 2009 Jan;165(1):1-9. doi: 10.1016/j.jsb.2008.09.006. Epub 2008 Sep 30.

PMID: 18926912 [PubMed - indexed for MEDLINE] Free PMC Article

4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus.

Zhang R, Hryc CF, Cong Y, Liu X, Jakana J, Gorchakov R, Baker ML, Weaver SC, Chiu W.

EMBO J. 2011 Aug 9;30(18):3854-63. doi: 10.1038/emboj.2011.261.

PMID: 21829169 [PubMed - indexed for MEDLINE] Free PMC Article

Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome.

LeBarron J, Grassucci RA, Shaikh TR, Baxter WT, Sengupta J, Frank J.

J Struct Biol. 2008 Oct;164(1):24-32. doi: 10.1016/j.jsb.2008.05.007. Epub 2008 Jun 18.

PMID: 18606549 [PubMed - indexed for MEDLINE] Free PMC Article

Practical performance evaluation of a 10k X 10k CCD for electron cryo-microscopy.

Bammes BE, Rochat RH, Jakana J, Chiu W.

J Struct Biol. 2011 Sep;175(3):384-93. doi: 10.1016/j.jsb.2011.05.012. Epub 2011 May 17.

PMID: 21619932 [PubMed - indexed for MEDLINE] Free PMC Article

Structural changes in dengue virus when exposed to a temperature of 37°C.

Fibriansah G, Ng TS, Kostyuchenko VA, Lee J, Lee S, Wang J, Lok SM.

J Virol. 2013 Jul;87(13):7585-92. doi: 10.1128/JVI.00757-13. Epub 2013 May 1.

PMID: 23637405 [PubMed - indexed for MEDLINE]

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.

PMID: 22405004 [PubMed - indexed for MEDLINE] Free PMC Article

Immature and mature dengue serotype 1 virus structures provide insight into the maturation process.

Kostyuchenko VA, Zhang Q, Tan JL, Ng TS, Lok SM.

J Virol. 2013 Jul;87(13):7700-7. doi: 10.1128/JVI.00197-13. Epub 2013 May 1.

PMID: 23637416 [PubMed - indexed for MEDLINE]

Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography.

Chang J, Liu X, Rochat RH, Baker ML, Chiu W.

Adv Exp Med Biol. 2012;726:49-90. doi: 10.1007/978-1-4614-0980-9_4. Review.

PMID: 22297510 [PubMed - indexed for MEDLINE]

Finite Element Model Updating Using Computational Intelligence Techniques: Applications to Structural Dynamics.

Tshilidzi Marwala

ISBN: 978-1-84996-322-0 (Print) 978-1-84996-323-7 (Online) June 4, 2010; DOI: 10.1007/978-1-84996-323-7

[Publisher - Springer] Preview

Militarized Conflict Modeling Using Computational Intelligence.

Tshilidzi Marwala, Monica Lagazio

ISBN: 978-0-85729-789-1 (Print) 978-0-85729-790-7 (Online), 2011; DOI: 10.1007/978-0-85729-790-7

[Publisher - Springer] Preview

Electron Cryomicroscopy and Three-dimensional Computer Reconstruction of Biological Molecules

Steven J Ludtke, Wah Chiu

DOI: 10.1002/9780470015902.a0002987.pub2; 15 JUN 2011

[Publisher - eLS. John Wiley & Sons Ltd, Chichester]

An automated procedure for detecting protein folds from sub-nanometer resolution electron density.

Khayat R, Lander GC, Johnson JE.

J Struct Biol. 2010 Jun;170(3):513-21. doi: 10.1016/j.jsb.2009.12.014. Epub 2009 Dec 22.

PMID: 20026407 [PubMed - indexed for MEDLINE] Free PMC Article

Cryo-EM structure of the mature dengue virus at 3.5-Å resolution.

Zhang X, Ge P, Yu X, Brannan JM, Bi G, Zhang Q, Schein S, Zhou ZH.

Nat Struct Mol Biol. 2013 Jan;20(1):105-10. doi: 10.1038/nsmb.2463. Epub 2012 Dec 16.

PMID: 23241927 [PubMed - indexed for MEDLINE] Free PMC Article

Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy.

Grigorieff N, Harrison SC.

Curr Opin Struct Biol. 2011 Apr;21(2):265-73. doi: 10.1016/j.sbi.2011.01.008. Epub 2011 Feb 18. Review.

PMID: 21333526 [PubMed - indexed for MEDLINE] Free PMC Article

An examination of the electrostatic interactions between the N-terminal tail of the Brome Mosaic Virus coat protein and encapsidated RNAs.

Ni P, Wang Z, Ma X, Das NC, Sokol P, Chiu W, Dragnea B, Hagan M, Kao CC.

J Mol Biol. 2012 Jun 22;419(5):284-300. doi: 10.1016/j.jmb.2012.03.023. Epub 2012 Apr 1.

PMID: 22472420 [PubMed - indexed for MEDLINE] Free PMC Article

Electron cryomicroscopy of biological macromolecules

T. S. Baker and R. Henderson.

International Tables for Crystallography (2012). Vol. F, ch. 19.6, pp. 593-614 doi:10.1107/97809553602060000872

Author's link

Visualization of bacteriophage T3 capsids with DNA incompletely packaged in vivo.

Fang PA, Wright ET, Weintraub ST, Hakala K, Wu W, Serwer P, Jiang W.

J Mol Biol. 2008 Dec 31;384(5):1384-99. doi: 10.1016/j.jmb.2008.10.012. Epub 2008 Oct 14.

PMID: 18952096 [PubMed - indexed for MEDLINE] Free PMC Article