Literature DB >> 17029842

AUTO3DEM--an automated and high throughput program for image reconstruction of icosahedral particles.

Xiaodong Yan1, Robert S Sinkovits, Timothy S Baker.   

Abstract

AUTO3DEM is an automation system designed to accelerate the computationally intensive process of three-dimensional structure determination from images of vitrified icosahedral virus particles. With minimal user input and intervention, AUTO3DEM manages the flow of data between the major image reconstruction programs, monitors the progress of the computations, and intelligently updates the input parameters as the resolution of the model is improved. It is designed to be used on any computer running the Linux or UNIX operating systems and can be run in parallel mode on multi-processor systems.

Mesh：

Year:  2006        PMID： 17029842      PMCID： PMC1847775          DOI： 10.1016/j.jsb.2006.08.007

Source DB:  PubMed          Journal:  J Struct Biol        ISSN： 1047-8477            Impact factor:   2.867


  14 in total

Review 1.  Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs.

Authors:  T S Baker; N H Olson; S D Fuller
Journal:  Microbiol Mol Biol Rev       Date:  1999-12       Impact factor: 11.056

2.  Leginon: an automated system for acquisition of images from vitreous ice specimens.

Authors:  B Carragher; N Kisseberth; D Kriegman; R A Milligan; C S Potter; J Pulokas; A Reilein
Journal:  J Struct Biol       Date:  2000-10       Impact factor: 2.867

3.  EMAN: semiautomated software for high-resolution single-particle reconstructions.

Authors:  S J Ludtke; P R Baldwin; W Chiu
Journal:  J Struct Biol       Date:  1999-12-01       Impact factor: 2.867

4.  Structure and assembly of large lipid-containing dsDNA viruses.

Authors:  X Yan; N H Olson; J L Van Etten; M Bergoin; M G Rossmann; T S Baker
Journal:  Nat Struct Biol       Date:  2000-02

Review 5.  Single-particle electron cryo-microscopy: towards atomic resolution.

Authors:  M van Heel; B Gowen; R Matadeen; E V Orlova; R Finn; T Pape; D Cohen; H Stark; R Schmidt; M Schatz; A Patwardhan
Journal:  Q Rev Biophys       Date:  2000-11       Impact factor: 5.318

6.  Resolution measurement in structures derived from single particles.

Authors:  N Grigorieff
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-10

7.  UCSF Chimera--a visualization system for exploratory research and analysis.

Authors:  Eric F Pettersen; Thomas D Goddard; Conrad C Huang; Gregory S Couch; Daniel M Greenblatt; Elaine C Meng; Thomas E Ferrin
Journal:  J Comput Chem       Date:  2004-10       Impact factor: 3.376

8.  Ab initio random model method facilitates 3D reconstruction of icosahedral particles.

Authors:  Xiaodong Yan; Kelly A Dryden; Jinghua Tang; Timothy S Baker
Journal:  J Struct Biol       Date:  2006-08-11       Impact factor: 2.867

9.  SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields.

Authors:  J Frank; M Radermacher; P Penczek; J Zhu; Y Li; M Ladjadj; A Leith
Journal:  J Struct Biol       Date:  1996 Jan-Feb       Impact factor: 2.867

10.  A model-based approach for determining orientations of biological macromolecules imaged by cryoelectron microscopy.

Authors:  T S Baker; R H Cheng
Journal:  J Struct Biol       Date:  1996 Jan-Feb       Impact factor: 2.867
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  137 in total

1.  A cryo-electron microscopy study identifies the complete H16.V5 epitope and reveals global conformational changes initiated by binding of the neutralizing antibody fragment.

Authors:  Hyunwook Lee; Sarah A Brendle; Stephanie M Bywaters; Jian Guan; Robert E Ashley; Joshua D Yoder; Alexander M Makhov; James F Conway; Neil D Christensen; Susan Hafenstein
Journal:  J Virol       Date:  2014-11-12       Impact factor: 5.103

2.  The herpes simplex virus 1 UL17 protein is the second constituent of the capsid vertex-specific component required for DNA packaging and retention.

Authors:  Katerina Toropova; Jamie B Huffman; Fred L Homa; James F Conway
Journal:  J Virol       Date:  2011-06-01       Impact factor: 5.103

3.  Backbone trace of partitivirus capsid protein from electron cryomicroscopy and homology modeling.

Authors:  Jinghua Tang; Junhua Pan; Wendy M Havens; Wendy F Ochoa; Tom S Y Guu; Said A Ghabrial; Max L Nibert; Yizhi Jane Tao; Timothy S Baker
Journal:  Biophys J       Date:  2010-07-21       Impact factor: 4.033

4.  Self-Assembly of an Alphavirus Core-like Particle Is Distinguished by Strong Intersubunit Association Energy and Structural Defects.

Authors:  Joseph Che-Yen Wang; Chao Chen; Vamseedhar Rayaprolu; Suchetana Mukhopadhyay; Adam Zlotnick
Journal:  ACS Nano       Date:  2015-08-21       Impact factor: 15.881

5.  Structural insight into African horsesickness virus infection.

Authors:  Violeta Manole; Pasi Laurinmäki; Wouter Van Wyngaardt; Christiaan A Potgieter; Isabella M Wright; Gert J Venter; Alberdina A van Dijk; B Trevor Sewell; Sarah J Butcher
Journal:  J Virol       Date:  2012-05-16       Impact factor: 5.103

6.  Molecular links between the E2 envelope glycoprotein and nucleocapsid core in Sindbis virus.

Authors:  Jinghua Tang; Joyce Jose; Paul Chipman; Wei Zhang; Richard J Kuhn; Timothy S Baker
Journal:  J Mol Biol       Date:  2011-10-04       Impact factor: 5.469

7.  Ab initio random model method facilitates 3D reconstruction of icosahedral particles.

Authors:  Xiaodong Yan; Kelly A Dryden; Jinghua Tang; Timothy S Baker
Journal:  J Struct Biol       Date:  2006-08-11       Impact factor: 2.867

8.  Infectious myonecrosis virus has a totivirus-like, 120-subunit capsid, but with fiber complexes at the fivefold axes.

Authors:  Jinghua Tang; Wendy F Ochoa; Robert S Sinkovits; Bonnie T Poulos; Said A Ghabrial; Donald V Lightner; Timothy S Baker; Max L Nibert
Journal:  Proc Natl Acad Sci U S A       Date:  2008-11-03       Impact factor: 11.205

9.  Mapping a neutralizing epitope onto the capsid of adeno-associated virus serotype 8.

Authors:  Brittney L Gurda; Christina Raupp; Ruth Popa-Wagner; Matthias Naumer; Norman H Olson; Robert Ng; Robert McKenna; Timothy S Baker; Jürgen A Kleinschmidt; Mavis Agbandje-McKenna
Journal:  J Virol       Date:  2012-05-16       Impact factor: 5.103

10.  Capsid antibodies to different adeno-associated virus serotypes bind common regions.

Authors:  Brittney L Gurda; Michael A DiMattia; Edward B Miller; Antonette Bennett; Robert McKenna; Wendy S Weichert; Christian D Nelson; Wei-jun Chen; Nicholas Muzyczka; Norman H Olson; Robert S Sinkovits; John A Chiorini; Sergei Zolotutkhin; Olga G Kozyreva; R Jude Samulski; Timothy S Baker; Colin R Parrish; Mavis Agbandje-McKenna
Journal:  J Virol       Date:  2013-06-12       Impact factor: 5.103
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