Publications by authors named "Matthew L Baker"

62Publications

Cryo-EM reveals ligand induced allostery underlying InsPR channel gating.

Cell Res 2018 12 23;28(12):1158-1170. Epub 2018 Nov 23.

Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX, 77030, USA.

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http://www.nature.com/articles/s41422-018-0108-5
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http://dx.doi.org/10.1038/s41422-018-0108-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6274648PMC
December 2018

Automation and assessment of de novo modeling with Pathwalking in near atomic resolution cryoEM density maps.

J Struct Biol 2018 12 17;204(3):555-563. Epub 2018 Sep 17.

Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States.

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https://linkinghub.elsevier.com/retrieve/pii/S10478477183025
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http://dx.doi.org/10.1016/j.jsb.2018.09.005DOI Listing
December 2018

Risk Factors for Knee Injury in Golf: A Systematic Review.

Sports Med 2017 Dec;47(12):2621-2639

Institute for Biomechanics, ETH Zürich, Leopold-Ruzicka-Weg 4, 8093, Zurich, Switzerland.

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http://dx.doi.org/10.1007/s40279-017-0780-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684267PMC
December 2017

Flexible Fitting of Atomic Models into Cryo-EM Density Maps Guided by Helix Correspondences.

Biophys J 2017 Jun;112(12):2479-2493

Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri.

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http://dx.doi.org/10.1016/j.bpj.2017.04.054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5479111PMC
June 2017

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

J Struct Biol 2016 12 17;196(3):289-298. Epub 2016 Jul 17.

Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2016.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5118137PMC
December 2016

Transversus abdominis plane block as the primary anesthetic for peritoneal dialysis catheter surgery.

J Clin Anesth 2016 Jun 16;31:182-8. Epub 2016 Apr 16.

Department of Anesthesiology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157-1009, United States.

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http://dx.doi.org/10.1016/j.jclinane.2016.01.028DOI Listing
June 2016

EMDataBank unified data resource for 3DEM.

Nucleic Acids Res 2016 Jan 17;44(D1):D396-403. Epub 2015 Nov 17.

Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA

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http://dx.doi.org/10.1093/nar/gkv1126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702818PMC
January 2016

Gating machinery of InsP3R channels revealed by electron cryomicroscopy.

Nature 2015 Nov 12;527(7578):336-41. Epub 2015 Oct 12.

Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, The University of Texas Medical School at Houston, 6431 Fannin Street, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature15249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804758PMC
November 2015

Domain organization and conformational plasticity of the G protein effector, PDE6.

J Biol Chem 2015 May 25;290(20):12833-43. Epub 2015 Mar 25.

From the Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 and.

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http://dx.doi.org/10.1074/jbc.M115.647636DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4432299PMC
May 2015

An atomic model of brome mosaic virus using direct electron detection and real-space optimization.

Nat Commun 2014 Sep 4;5:4808. Epub 2014 Sep 4.

1] National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA [2] Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/ncomms5808DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155512PMC
September 2014

Protruding knob-like proteins violate local symmetries in an icosahedral marine virus.

Nat Commun 2014 Jul 2;5:4278. Epub 2014 Jul 2.

Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/ncomms5278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4102127PMC
July 2014

Multiple functional roles of the accessory I-domain of bacteriophage P22 coat protein revealed by NMR structure and CryoEM modeling.

Structure 2014 Jun 15;22(6):830-41. Epub 2014 May 15.

Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA. Electronic address:

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http://dx.doi.org/10.1016/j.str.2014.04.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4068711PMC
June 2014

Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling.

Proc Natl Acad Sci U S A 2013 Jul 9;110(30):12301-6. Epub 2013 Jul 9.

National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1073/pnas.1309947110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3725109PMC
July 2013

TanCAR: A Novel Bispecific Chimeric Antigen Receptor for Cancer Immunotherapy.

Mol Ther Nucleic Acids 2013 Jul 9;2:e105. Epub 2013 Jul 9.

1] Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and The Methodist Hospital, Houston, Texas, USA [2] Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas, USA [3] Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.

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http://dx.doi.org/10.1038/mtna.2013.32DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3731887PMC
July 2013

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

Biopolymers 2012 Sep;97(9):655-68

Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1002/bip.22065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3899894PMC
September 2012

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

Structure 2012 Mar;20(3):450-63

National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.str.2012.01.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3307788PMC
March 2012

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

Adv Exp Med Biol 2012 ;726:49-90

Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.

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http://link.springer.com/10.1007/978-1-4614-0980-9_4
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http://dx.doi.org/10.1007/978-1-4614-0980-9_4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954858PMC
April 2012

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

EMBO J 2011 Aug 9;30(18):3854-63. Epub 2011 Aug 9.

Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, USA.

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http://emboj.embopress.org/cgi/doi/10.1038/emboj.2011.261
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http://dx.doi.org/10.1038/emboj.2011.261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3173789PMC
August 2011

Crystal structure of the cytoplasmic N-terminal domain of subunit I, a homolog of subunit a, of V-ATPase.

J Mol Biol 2011 Sep 22;412(1):14-21. Epub 2011 Jul 22.

Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.jmb.2011.07.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207611PMC
September 2011

Modeling protein structure at near atomic resolutions with Gorgon.

J Struct Biol 2011 May 4;174(2):360-73. Epub 2011 Feb 4.

National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.jsb.2011.01.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3078171PMC
May 2011

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

Proc Natl Acad Sci U S A 2011 Jan 10;108(4):1355-60. Epub 2011 Jan 10.

National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1073/pnas.1015739108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029737PMC
January 2011

EMDataBank.org: unified data resource for CryoEM.

Nucleic Acids Res 2011 Jan 8;39(Database issue):D456-64. Epub 2010 Oct 8.

Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA.

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http://dx.doi.org/10.1093/nar/gkq880DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013769PMC
January 2011

Analyses of subnanometer resolution cryo-EM density maps.

Methods Enzymol 2010 ;483:1-29

National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.

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http://dx.doi.org/10.1016/S0076-6879(10)83001-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3107677PMC
January 2011

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

Nat Protoc 2010 Sep 30;5(10):1697-708. Epub 2010 Sep 30.

National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.

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http://dx.doi.org/10.1038/nprot.2010.126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3107675PMC
September 2010

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

Nat Struct Mol Biol 2010 Jul 13;17(7):830-6. Epub 2010 Jun 13.

National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.

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http://dx.doi.org/10.1038/nsmb.1823DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2924429PMC
July 2010

Tracing conformational changes in proteins.

BMC Struct Biol 2010 May 17;10 Suppl 1:S1. Epub 2010 May 17.

Department of Computer Science, Rice University, Houston, TX 77005, USA.

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http://dx.doi.org/10.1186/1472-6807-10-S1-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873824PMC
May 2010

4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement.

Proc Natl Acad Sci U S A 2010 Mar 1;107(11):4967-72. Epub 2010 Mar 1.

National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemsitry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030.

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http://dx.doi.org/10.1073/pnas.0913774107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841888PMC
March 2010

Mechanism of folding chamber closure in a group II chaperonin.

Nature 2010 Jan;463(7279):379-83

Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature08701DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834796PMC
January 2010

Refinement of protein structures into low-resolution density maps using rosetta.

J Mol Biol 2009 Sep 8;392(1):181-90. Epub 2009 Jul 8.

Department of Biochemistry, University of Washington, Seattle, 98195, USA.

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http://dx.doi.org/10.1016/j.jmb.2009.07.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3899897PMC
September 2009

Rotavirus architecture at subnanometer resolution.

J Virol 2009 Feb 26;83(4):1754-66. Epub 2008 Nov 26.

National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1128/JVI.01855-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643745PMC
February 2009

Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel.

Proc Natl Acad Sci U S A 2008 Jul 10;105(28):9610-5. Epub 2008 Jul 10.

National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

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http://dx.doi.org/10.1073/pnas.0803189105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2474495PMC
July 2008

De novo backbone trace of GroEL from single particle electron cryomicroscopy.

Structure 2008 Mar;16(3):441-8

National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.str.2008.02.007DOI Listing
March 2008

Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy.

Nature 2008 Feb;451(7182):1130-4

Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.

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http://dx.doi.org/10.1038/nature06665DOI Listing
February 2008

Identification of secondary structure elements in intermediate-resolution density maps.

Structure 2007 Jan;15(1):7-19

National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.str.2006.11.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1810566PMC
January 2007

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

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

National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.0020146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1626159PMC
October 2006

Cryoelectron microscopy of protein IX-modified adenoviruses suggests a new position for the C terminus of protein IX.

J Virol 2006 Dec 20;80(23):11881-6. Epub 2006 Sep 20.

Program in Structural and Computational Biology and Molecular Biophysics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.

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http://jvi.asm.org/cgi/doi/10.1128/JVI.01471-06
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http://dx.doi.org/10.1128/JVI.01471-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1642590PMC
December 2006

Automated segmentation of molecular subunits in electron cryomicroscopy density maps.

J Struct Biol 2006 Dec 14;156(3):432-41. Epub 2006 Jun 14.

National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.jsb.2006.05.013DOI Listing
December 2006

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

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

Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, QB3, 1700 4th Street, Suite 503B, University of California at San Francisco, San Francisco, CA 94143-2552, USA.

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http://dx.doi.org/10.1016/j.jmb.2006.01.062DOI Listing
April 2006

Structural biology of cellular machines.

Trends Cell Biol 2006 Mar 3;16(3):144-50. Epub 2006 Feb 3.

National Center for Macromolecular Imaging and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.tcb.2006.01.002DOI Listing
March 2006

Common ancestry of herpesviruses and tailed DNA bacteriophages.

J Virol 2005 Dec;79(23):14967-70

National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1128/JVI.79.23.14967-14970.2005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1287596PMC
December 2005

Electron cryomicroscopy of biological machines at subnanometer resolution.

Structure 2005 Mar;13(3):363-72

National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1016/j.str.2004.12.016DOI Listing
March 2005

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

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

Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, Mission Bay Genentech Hall, 600 16th Street, Suite N472D, University of California, San Francisco, CA 94143, USA.

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http://www.salilab.org/pdf/Topf_JStructBiol_2005.pdf
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http://linkinghub.elsevier.com/retrieve/pii/S104784770400217
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http://dx.doi.org/10.1016/j.jsb.2004.11.004DOI Listing
February 2005

A 9 angstroms single particle reconstruction from CCD captured images on a 200 kV electron cryomicroscope.

J Struct Biol 2004 Aug;147(2):116-27

Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.jsb.2004.02.004DOI Listing
August 2004

Applications of a bilateral denoising filter in biological electron microscopy.

J Struct Biol 2003 Oct-Nov;144(1-2):114-22

Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.jsb.2003.09.028DOI Listing
July 2004

Architecture of the herpes simplex virus major capsid protein derived from structural bioinformatics.

J Mol Biol 2003 Aug;331(2):447-56

National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/s0022-2836(03)00696-xDOI Listing
August 2003

Structure of the herpesvirus major capsid protein.

EMBO J 2003 Feb;22(4):757-65

Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Graduate Program in Structural and Computational Biology, Baylor College of Medicine, Houston, TX 77030, USA.

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http://emboj.embopress.org/cgi/doi/10.1093/emboj/cdg086
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http://dx.doi.org/10.1093/emboj/cdg086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC145446PMC
February 2003

Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions.

Nat Struct Biol 2003 Feb;10(2):131-5

National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nsb891DOI Listing
February 2003

The skeletal muscle Ca2+ release channel has an oxidoreductase-like domain.

Proc Natl Acad Sci U S A 2002 Sep 6;99(19):12155-60. Epub 2002 Sep 6.

Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

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http://dx.doi.org/10.1073/pnas.182058899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC129414PMC
September 2002

Deriving folds of macromolecular complexes through electron cryomicroscopy and bioinformatics approaches.

Curr Opin Struct Biol 2002 Apr;12(2):263-9

Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1016/s0959-440x(02)00319-6DOI Listing
April 2002