Literature DB >> 23211764

Data management challenges in three-dimensional EM.

Ardan Patwardhan1, José-Maria Carazo, Bridget Carragher, Richard Henderson, J Bernard Heymann, Emma Hill, Grant J Jensen, Ingvar Lagerstedt, Catherine L Lawson, Steven J Ludtke, David Mastronarde, William J Moore, Alan Roseman, Peter Rosenthal, Carlos-Oscar S Sorzano, Eduardo Sanz-García, Sjors H W Scheres, Sriram Subramaniam, John Westbrook, Martyn Winn, Jason R Swedlow, Gerard J Kleywegt.   

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Year:  2012        PMID: 23211764      PMCID: PMC4048199          DOI: 10.1038/nsmb.2426

Source DB:  PubMed          Journal:  Nat Struct Mol Biol        ISSN: 1545-9985            Impact factor:   15.369


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  21 in total

1.  New electron microscopy database and deposition system.

Authors:  Mohamed Tagari; Richard Newman; Monica Chagoyen; Jose Maria Carazo; Kim Henrick
Journal:  Trends Biochem Sci       Date:  2002-11       Impact factor: 13.807

2.  Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy.

Authors:  Peter B Rosenthal; Richard Henderson
Journal:  J Mol Biol       Date:  2003-10-31       Impact factor: 5.469

Review 3.  Structural characterization of proteins and complexes using small-angle X-ray solution scattering.

Authors:  Haydyn D T Mertens; Dmitri I Svergun
Journal:  J Struct Biol       Date:  2010-06-15       Impact factor: 2.867

4.  Bsoft: image processing and molecular modeling for electron microscopy.

Authors:  J Bernard Heymann; David M Belnap
Journal:  J Struct Biol       Date:  2006-06-28       Impact factor: 2.867

Review 5.  MRC image processing programs.

Authors:  R A Crowther; R Henderson; J M Smith
Journal:  J Struct Biol       Date:  1996 Jan-Feb       Impact factor: 2.867

6.  Metadata matters: access to image data in the real world.

Authors:  Melissa Linkert; Curtis T Rueden; Chris Allan; Jean-Marie Burel; Will Moore; Andrew Patterson; Brian Loranger; Josh Moore; Carlos Neves; Donald Macdonald; Aleksandra Tarkowska; Caitlin Sticco; Emma Hill; Mike Rossner; Kevin W Eliceiri; Jason R Swedlow
Journal:  J Cell Biol       Date:  2010-05-31       Impact factor: 10.539

7.  Role of dimerization and substrate exclusion in the regulation of bone morphogenetic protein-1 and mammalian tolloid.

Authors:  Richard Berry; Thomas A Jowitt; Johanna Ferrand; Manfred Roessle; J Günter Grossmann; Elizabeth G Canty-Laird; Richard A Kammerer; Karl E Kadler; Clair Baldock
Journal:  Proc Natl Acad Sci U S A       Date:  2009-05-08       Impact factor: 11.205

8.  Appion: an integrated, database-driven pipeline to facilitate EM image processing.

Authors:  Gabriel C Lander; Scott M Stagg; Neil R Voss; Anchi Cheng; Denis Fellmann; James Pulokas; Craig Yoshioka; Christopher Irving; Anke Mulder; Pick-Wei Lau; Dmitry Lyumkis; Clinton S Potter; Bridget Carragher
Journal:  J Struct Biol       Date:  2009-04       Impact factor: 2.867

9.  PDBe: Protein Data Bank in Europe.

Authors:  S Velankar; Y Alhroub; C Best; S Caboche; M J Conroy; J M Dana; M A Fernandez Montecelo; G van Ginkel; A Golovin; S P Gore; A Gutmanas; P Haslam; P M S Hendrickx; E Heuson; M Hirshberg; M John; I Lagerstedt; S Mir; L E Newman; T J Oldfield; A Patwardhan; L Rinaldi; G Sahni; E Sanz-García; S Sen; R Slowley; A Suarez-Uruena; G J Swaminathan; M F Symmons; W F Vranken; M Wainwright; G J Kleywegt
Journal:  Nucleic Acids Res       Date:  2011-11-21       Impact factor: 16.971

10.  Tilt-pair analysis of images from a range of different specimens in single-particle electron cryomicroscopy.

Authors:  Richard Henderson; Shaoxia Chen; James Z Chen; Nikolaus Grigorieff; Lori A Passmore; Luciano Ciccarelli; John L Rubinstein; R Anthony Crowther; Phoebe L Stewart; Peter B Rosenthal
Journal:  J Mol Biol       Date:  2011-09-12       Impact factor: 5.469

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  25 in total

1.  Reducing cryoEM file storage using lossy image formats.

Authors:  Edward T Eng; Mykhailo Kopylov; Carl J Negro; Sarkis Dallaykan; William J Rice; Kelsey D Jordan; Kotaro Kelley; Bridget Carragher; Clinton S Potter
Journal:  J Struct Biol       Date:  2019-05-21       Impact factor: 2.867

2.  Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies.

Authors:  Pilar Cossio; Gerhard Hummer
Journal:  J Struct Biol       Date:  2013-10-24       Impact factor: 2.867

Review 3.  Big data in cryoEM: automated collection, processing and accessibility of EM data.

Authors:  Philip R Baldwin; Yong Zi Tan; Edward T Eng; William J Rice; Alex J Noble; Carl J Negro; Michael A Cianfrocco; Clinton S Potter; Bridget Carragher
Journal:  Curr Opin Microbiol       Date:  2017-10-31       Impact factor: 7.934

4.  A detailed look at the cytoskeletal architecture of the Giardia lamblia ventral disc.

Authors:  Joanna R Brown; Cindi L Schwartz; John M Heumann; Scott C Dawson; Andreas Hoenger
Journal:  J Struct Biol       Date:  2016-01-25       Impact factor: 2.867

5.  EMPIAR: a public archive for raw electron microscopy image data.

Authors:  Andrii Iudin; Paul K Korir; José Salavert-Torres; Gerard J Kleywegt; Ardan Patwardhan
Journal:  Nat Methods       Date:  2016-03-21       Impact factor: 28.547

6.  Validation of 3D EM Reconstructions: The Phantom in the Noise.

Authors:  J Bernard Heymann
Journal:  AIMS Biophys       Date:  2015

7.  ValiDichro: a website for validating and quality control of protein circular dichroism spectra.

Authors:  Benjamin Woollett; Lee Whitmore; Robert W Janes; B A Wallace
Journal:  Nucleic Acids Res       Date:  2013-04-26       Impact factor: 16.971

8.  Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.

Authors:  Helen M Berman; Paul D Adams; Alexandre A Bonvin; Stephen K Burley; Bridget Carragher; Wah Chiu; Frank DiMaio; Thomas E Ferrin; Margaret J Gabanyi; Thomas D Goddard; Patrick R Griffin; Juergen Haas; Christian A Hanke; Jeffrey C Hoch; Gerhard Hummer; Genji Kurisu; Catherine L Lawson; Alexander Leitner; John L Markley; Jens Meiler; Gaetano T Montelione; George N Phillips; Thomas Prisner; Juri Rappsilber; David C Schriemer; Torsten Schwede; Claus A M Seidel; Timothy S Strutzenberg; Dmitri I Svergun; Emad Tajkhorshid; Jill Trewhella; Brinda Vallat; Sameer Velankar; Geerten W Vuister; Benjamin Webb; John D Westbrook; Kate L White; Andrej Sali
Journal:  Structure       Date:  2019-11-25       Impact factor: 5.006

Review 9.  Databases and Archiving for CryoEM.

Authors:  A Patwardhan; C L Lawson
Journal:  Methods Enzymol       Date:  2016-06-16       Impact factor: 1.600

10.  The role of structural bioinformatics resources in the era of integrative structural biology.

Authors:  Aleksandras Gutmanas; Thomas J Oldfield; Ardan Patwardhan; Sanchayita Sen; Sameer Velankar; Gerard J Kleywegt
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-04-19
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