Literature DB >> 32645578

Local resolution estimates of cryoEM reconstructions.

J L Vilas1, J B Heymann2, H D Tagare1, E Ramirez-Aportela3, J M Carazo3, Cos Sorzano4.   

Abstract

The field of cryoEM has quickly advanced in last years with the new biochemical, technological, methodological and computational developments. It has allowed significant progresses in Structural Biology, typically reaching quasi-atomic resolutions in the reconstructed maps. However, this rapid advance has also generated new questions relevant to resolution estimates. The global resolution metrics and their criteria have been deeply discussed in the last decade, but despite that, it remains as an important issue in the field. Recently, the introduction of local resolution measurements has changed how cryoEM reconstructions are interpreted, providing information about the existence of heterogeneity, flexibility, and angular assignment errors, and using it as a tool to aid in modeling. In this review we revisit the concept of local resolution and the different algorithms in the current state of the art. However, the concept of local resolution is not uniquely defined, and each implementation measures different features. This may lead to inappropriate interpretation of local resolution maps. Hence, a set of good practices is provided in this review to avoid misleading and over-interpretation of the reconstructions.
Copyright © 2020 Elsevier Ltd. All rights reserved.

Entities:  

Year:  2020        PMID: 32645578      PMCID: PMC7666004          DOI: 10.1016/j.sbi.2020.06.005

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  18 in total

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Journal:  J Comput Chem       Date:  2004-10       Impact factor: 3.376

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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 4.  A review of resolution measures and related aspects in 3D Electron Microscopy.

Authors:  C O S Sorzano; J Vargas; J Otón; V Abrishami; J M de la Rosa-Trevín; J Gómez-Blanco; J L Vilas; R Marabini; J M Carazo
Journal:  Prog Biophys Mol Biol       Date:  2016-09-22       Impact factor: 3.667

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Authors:  M Unser; B L Trus; A C Steven
Journal:  Ultramicroscopy       Date:  1987       Impact factor: 2.689

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

7.  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

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Journal:  Nature       Date:  2017-07-12       Impact factor: 49.962

9.  DeepRes: a new deep-learning- and aspect-based local resolution method for electron-microscopy maps.

Authors:  Erney Ramírez-Aportela; Javier Mota; Pablo Conesa; Jose Maria Carazo; Carlos Oscar S Sorzano
Journal:  IUCrJ       Date:  2019-09-18       Impact factor: 4.769

10.  Measuring local-directional resolution and local anisotropy in cryo-EM maps.

Authors:  Jose Luis Vilas; Hemant D Tagare; Javier Vargas; Jose Maria Carazo; Carlos Oscar S Sorzano
Journal:  Nat Commun       Date:  2020-01-02       Impact factor: 14.919

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  4 in total

Review 1.  Emerging Themes in CryoEM─Single Particle Analysis Image Processing.

Authors:  Jose Luis Vilas; Jose Maria Carazo; Carlos Oscar S Sorzano
Journal:  Chem Rev       Date:  2022-07-04       Impact factor: 72.087

2.  Structural basis for SARS-CoV-2 envelope protein recognition of human cell junction protein PALS1.

Authors:  Jin Chai; Yuanheng Cai; Changxu Pang; Liguo Wang; Sean McSweeney; John Shanklin; Qun Liu
Journal:  Nat Commun       Date:  2021-06-08       Impact factor: 14.919

3.  Pore structure controls stability and molecular flux in engineered protein cages.

Authors:  Lachlan S R Adamson; Nuren Tasneem; Michael P Andreas; William Close; Eric N Jenner; Taylor N Szyszka; Reginald Young; Li Chen Cheah; Alexander Norman; Hugo I MacDermott-Opeskin; Megan L O'Mara; Frank Sainsbury; Tobias W Giessen; Yu Heng Lau
Journal:  Sci Adv       Date:  2022-02-04       Impact factor: 14.136

4.  Cryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state.

Authors:  Wu Liu; Martien Schoonen; Tong Wang; Sean McSweeney; Qun Liu
Journal:  Commun Biol       Date:  2022-03-23
  4 in total

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