Literature DB >> 33950394

Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods.

Carlos Oscar S Sorzano1, Amaya Jiménez-Moreno2, David Maluenda2, Erney Ramírez-Aportela2, Marta Martínez2, Ana Cuervo2, Robert Melero2, Jose Javier Conesa2, Ruben Sánchez-García2, David Strelak2, Jiri Filipovic3, Estrella Fernández-Giménez2, Federico de Isidro-Gómez2, David Herreros2, Pablo Conesa2, Laura Del Caño2, Yunior Fonseca2, Jorge Jiménez de la Morena2, Jose Ramon Macías2, Patricia Losana2, Roberto Marabini4, Jose-Maria Carazo2.   

Abstract

Cryo-electron microscopy has established as a mature structural biology technique to elucidate the three-dimensional structure of biological macromolecules. The Coulomb potential of the sample is imaged by an electron beam, and fast semi-conductor detectors produce movies of the sample under study. These movies have to be further processed by a whole pipeline of image-processing algorithms that produce the final structure of the macromolecule. In this chapter, we illustrate this whole processing pipeline putting in value the strength of "meta algorithms," which are the combination of several algorithms, each one with different mathematical rationale, in order to distinguish correctly from incorrectly estimated parameters. We show how this strategy leads to superior performance of the whole pipeline as well as more confident assessments about the reconstructed structures. The "meta algorithms" strategy is common to many fields and, in particular, it has provided excellent results in bioinformatics. We illustrate this combination using the workflow engine, Scipion.

Keywords:  Cryo-electron microscopy; Image processing; Scipion; Single particle

Year:  2021        PMID: 33950394     DOI: 10.1007/978-1-0716-1406-8_13

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  51 in total

Review 1.  Challenges and opportunities in cryo-EM single-particle analysis.

Authors:  Dmitry Lyumkis
Journal:  J Biol Chem       Date:  2019-02-25       Impact factor: 5.157

Review 2.  Computational methods for analyzing conformational variability of macromolecular complexes from cryo-electron microscopy images.

Authors:  Slavica Jonić
Journal:  Curr Opin Struct Biol       Date:  2017-01-11       Impact factor: 6.809

3.  Drug designers embrace cryo-EM.

Authors:  Michael Eisenstein
Journal:  Nat Biotechnol       Date:  2018-07-06       Impact factor: 54.908

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

Review 5.  Miniaturizing EM Sample Preparation: Opportunities, Challenges, and "Visual Proteomics".

Authors:  Stefan A Arnold; Shirley A Müller; Claudio Schmidli; Anastasia Syntychaki; Luca Rima; Mohamed Chami; Henning Stahlberg; Kenneth N Goldie; Thomas Braun
Journal:  Proteomics       Date:  2018-03       Impact factor: 3.984

6.  MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps.

Authors:  Jose Luis Vilas; Josué Gómez-Blanco; Pablo Conesa; Roberto Melero; José Miguel de la Rosa-Trevín; Joaquin Otón; Jesús Cuenca; Roberto Marabini; José María Carazo; Javier Vargas; Carlos Oscar S Sorzano
Journal:  Structure       Date:  2018-01-27       Impact factor: 5.006

Review 7.  Cryo-EM for Small Molecules Discovery, Design, Understanding, and Application.

Authors:  Giovanna Scapin; Clinton S Potter; Bridget Carragher
Journal:  Cell Chem Biol       Date:  2018-08-09       Impact factor: 8.116

8.  The first single particle analysis Map Challenge: A summary of the assessments.

Authors:  J Bernard Heymann; Roberto Marabini; Mohsen Kazemi; Carlos Oscar S Sorzano; Maya Holmdahl; Joshua H Mendez; Scott M Stagg; Slavica Jonic; Eugene Palovcak; Jean-Paul Armache; Jianhua Zhao; Yifan Cheng; Grigore Pintilie; Wah Chiu; Ardan Patwardhan; Jose-Maria Carazo
Journal:  J Struct Biol       Date:  2018-08-13       Impact factor: 2.867

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

Authors:  Zhao Wang; Corey F Hryc; Benjamin Bammes; Pavel V Afonine; Joanita Jakana; Dong-Hua Chen; Xiangan Liu; Matthew L Baker; Cheng Kao; Steven J Ludtke; Michael F Schmid; Paul D Adams; Wah Chiu
Journal:  Nat Commun       Date:  2014-09-04       Impact factor: 14.919

Review 10.  Developments, applications, and prospects of cryo-electron microscopy.

Authors:  Xu Benjin; Liu Ling
Journal:  Protein Sci       Date:  2019-12-26       Impact factor: 6.725

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  3 in total

1.  On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy.

Authors:  C O S Sorzano; A Jiménez-Moreno; D Maluenda; M Martínez; E Ramírez-Aportela; J Krieger; R Melero; A Cuervo; J Conesa; J Filipovic; P Conesa; L Del Caño; Y C Fonseca; J Jiménez-de la Morena; P Losana; R Sánchez-García; D Strelak; E Fernández-Giménez; F P de Isidro-Gómez; D Herreros; J L Vilas; R Marabini; J M Carazo
Journal:  Acta Crystallogr D Struct Biol       Date:  2022-03-16       Impact factor: 7.652

2.  Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding.

Authors:  Helder Veras Ribeiro-Filho; Gabriel Ernesto Jara; Fernanda Aparecida Heleno Batista; Gabriel Ravanhani Schleder; Celisa Caldana Costa Tonoli; Adriana Santos Soprano; Samuel Leite Guimarães; Antonio Carlos Borges; Alexandre Cassago; Marcio Chaim Bajgelman; Rafael Elias Marques; Daniela Barretto Barbosa Trivella; Kleber Gomes Franchini; Ana Carolina Migliorini Figueira; Celso Eduardo Benedetti; Paulo Sergio Lopes-de-Oliveira
Journal:  PLoS Comput Biol       Date:  2022-05-12       Impact factor: 4.779

3.  The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation.

Authors:  Tiziana Ginex; Clara Marco-Marín; Miłosz Wieczór; Carlos P Mata; James Krieger; Paula Ruiz-Rodriguez; Maria Luisa López-Redondo; Clara Francés-Gómez; Roberto Melero; Carlos Óscar Sánchez-Sorzano; Marta Martínez; Nadine Gougeard; Alicia Forcada-Nadal; Sara Zamora-Caballero; Roberto Gozalbo-Rovira; Carla Sanz-Frasquet; Rocío Arranz; Jeronimo Bravo; Vicente Rubio; Alberto Marina; Ron Geller; Iñaki Comas; Carmen Gil; Mireia Coscolla; Modesto Orozco; José Luis Llácer; Jose-Maria Carazo
Journal:  PLoS Pathog       Date:  2022-07-11       Impact factor: 7.464

  3 in total

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