Literature DB >> 28971542

Scipion web tools: Easy to use cryo-EM image processing over the web.

Pablo Conesa Mingo1, José Gutierrez1, Adrián Quintana1, José Miguel de la Rosa Trevín1, Airén Zaldívar-Peraza1, Jesús Cuenca Alba1, Mohsen Kazemi1, Javier Vargas1, Laura Del Cano1, Joan Segura1, Carlos Oscar S Sorzano1, Jose María Carazo1.   

Abstract

Macromolecular structural determination by Electron Microscopy under cryogenic conditions is revolutionizing the field of structural biology, interesting a large community of potential users. Still, the path from raw images to density maps is complex, and sophisticated image processing suites are required in this process, often demanding the installation and understanding of different software packages. Here, we present Scipion Web Tools, a web-based set of tools/workflows derived from the Scipion image processing framework, specially tailored to nonexpert users in need of very precise answers at several key stages of the structural elucidation process.
© 2017 The Protein Society.

Keywords:  cryo-electron microscopy; validation; visualization; web tools; workflow

Mesh：

Year:  2017        PMID： 28971542      PMCID： PMC5734268          DOI： 10.1002/pro.3315

Source DB:  PubMed          Journal:  Protein Sci        ISSN： 0961-8368            Impact factor:   6.725


  18 in total

Review 1.  Validating maps from single particle electron cryomicroscopy.

Authors:  Peter B Rosenthal; John L Rubinstein
Journal:  Curr Opin Struct Biol       Date:  2015-11-19       Impact factor: 6.809

2.  Alignment of direct detection device micrographs using a robust Optical Flow approach.

Authors:  Vahid Abrishami; Javier Vargas; Xueming Li; Yifan Cheng; Roberto Marabini; Carlos Óscar Sánchez Sorzano; José María Carazo
Journal:  J Struct Biol       Date:  2015-02-12       Impact factor: 2.867

3.  ScipionCloud: An integrative and interactive gateway for large scale cryo electron microscopy image processing on commercial and academic clouds.

Authors:  Jesús Cuenca-Alba; Laura Del Cano; Josué Gómez Blanco; José Miguel de la Rosa Trevín; Pablo Conesa Mingo; Roberto Marabini; Carlos Oscar S Sorzano; Jose María Carazo
Journal:  J Struct Biol       Date:  2017-06-26       Impact factor: 2.867

4.  Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy.

Authors:  J M de la Rosa-Trevín; A Quintana; L Del Cano; A Zaldívar; I Foche; J Gutiérrez; J Gómez-Blanco; J Burguet-Castell; J Cuenca-Alba; V Abrishami; J Vargas; J Otón; G Sharov; J L Vilas; J Navas; P Conesa; M Kazemi; R Marabini; C O S Sorzano; J M Carazo
Journal:  J Struct Biol       Date:  2016-04-20       Impact factor: 2.867

5.  Single particle electron cryomicroscopy: trends, issues and future perspective.

Authors:  Kutti R Vinothkumar; Richard Henderson
Journal:  Q Rev Biophys       Date:  2016-07-22       Impact factor: 5.318

6.  One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions.

Authors:  Giovanni Cardone; J Bernard Heymann; Alasdair C Steven
Journal:  J Struct Biol       Date:  2013-08-14       Impact factor: 2.867

7.  Overview of the CCP4 suite and current developments.

Authors:  Martyn D Winn; Charles C Ballard; Kevin D Cowtan; Eleanor J Dodson; Paul Emsley; Phil R Evans; Ronan M Keegan; Eugene B Krissinel; Andrew G W Leslie; Airlie McCoy; Stuart J McNicholas; Garib N Murshudov; Navraj S Pannu; Elizabeth A Potterton; Harold R Powell; Randy J Read; Alexei Vagin; Keith S Wilson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2011-03-18

8.  Quantifying the local resolution of cryo-EM density maps.

Authors:  Alp Kucukelbir; Fred J Sigworth; Hemant D Tagare
Journal:  Nat Methods       Date:  2013-11-10       Impact factor: 28.547

9.  3did: a catalog of domain-based interactions of known three-dimensional structure.

Authors:  Roberto Mosca; Arnaud Céol; Amelie Stein; Roger Olivella; Patrick Aloy
Journal:  Nucleic Acids Res       Date:  2013-09-29       Impact factor: 16.971

10.  NGL Viewer: a web application for molecular visualization.

Authors:  Alexander S Rose; Peter W Hildebrand
Journal:  Nucleic Acids Res       Date:  2015-04-29       Impact factor: 16.971
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  5 in total

Review 1.  Local resolution estimates of cryoEM reconstructions.

Authors:  J L Vilas; J B Heymann; H D Tagare; E Ramirez-Aportela; J M Carazo; Cos Sorzano
Journal:  Curr Opin Struct Biol       Date:  2020-07-07       Impact factor: 6.809

2.  Cryo-EM Structure of a Kinetically Trapped Dodecameric Portal Protein from the Pseudomonas-phage PaP3.

Authors:  Chun-Feng David Hou; Nicholas A Swanson; Fenglin Li; Ruoyu Yang; Ravi K Lokareddy; Gino Cingolani
Journal:  J Mol Biol       Date:  2022-03-09       Impact factor: 6.151

3.  cisTEM, user-friendly software for single-particle image processing.

Authors:  Timothy Grant; Alexis Rohou; Nikolaus Grigorieff
Journal:  Elife       Date:  2018-03-07       Impact factor: 8.140

4.  West-Life: A Virtual Research Environment for structural biology.

Authors:  Chris Morris; Paolo Andreetto; Lucia Banci; Alexandre M J J Bonvin; Grzegorz Chojnowski; Laura Del Cano; José Marıa Carazo; Pablo Conesa; Susan Daenke; George Damaskos; Andrea Giachetti; Natalie E C Haley; Maarten L Hekkelman; Philipp Heuser; Robbie P Joosten; Daniel Kouřil; Aleš Křenek; Tomáš Kulhánek; Victor S Lamzin; Nurul Nadzirin; Anastassis Perrakis; Antonio Rosato; Fiona Sanderson; Joan Segura; Joerg Schaarschmidt; Egor Sobolev; Sergio Traldi; Mikael E Trellet; Sameer Velankar; Marco Verlato; Martyn Winn
Journal:  J Struct Biol X       Date:  2019-02-26

5.  Structures of pseudorabies virus capsids.

Authors:  Guosong Wang; Zhenghui Zha; Pengfei Huang; Hui Sun; Yang Huang; Maozhou He; Tian Chen; Lina Lin; Zhenqin Chen; Zhibo Kong; Yuqiong Que; Tingting Li; Ying Gu; Hai Yu; Jun Zhang; Qingbing Zheng; Yixin Chen; Shaowei Li; Ningshao Xia
Journal:  Nat Commun       Date:  2022-03-22       Impact factor: 17.694
  5 in total

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