Literature DB >> 30145327

A new algorithm for high-resolution reconstruction of single particles by electron microscopy.

C O S Sorzano1, J Vargas2, J M de la Rosa-Trevín3, A Jiménez4, D Maluenda4, R Melero4, M Martínez4, E Ramírez-Aportela4, P Conesa4, J L Vilas4, R Marabini5, J M Carazo4.   

Abstract

The Map Challenge organized by the Electron Microscopy Data Bank has prompted the development of an Xmipp high resolution reconstruction protocol (which we will refer to as highres) that is integrated in the software platform Scipion. In this work we describe the details of the image angular alignment and map reconstruction steps in our new method. This algorithm is similar to the standard projection matching approach with some important modifications, especially in the area of detecting significant features in the reconstructed volume. We show that the new method is able to produce higher resolution maps than the current de facto standard as measured by the Fourier Shell Correlation, the Monogenic Local Resolution and EMRinger.
Copyright © 2018 Elsevier Inc. All rights reserved.

Keywords:  3D reconstruction; Angular assignment; Image processing; Volume restoration

Mesh:

Year:  2018        PMID: 30145327     DOI: 10.1016/j.jsb.2018.08.002

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


  8 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.  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

3.  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

4.  Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures.

Authors:  Roberto Melero; Carlos Oscar S Sorzano; Brent Foster; José-Luis Vilas; Marta Martínez; Roberto Marabini; Erney Ramírez-Aportela; Ruben Sanchez-Garcia; David Herreros; Laura Del Caño; Patricia Losana; Yunior C Fonseca-Reyna; Pablo Conesa; Daniel Wrapp; Pablo Chacon; Jason S McLellan; Hemant D Tagare; Jose-Maria Carazo
Journal:  IUCrJ       Date:  2020-09-29       Impact factor: 4.769

5.  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

6.  Higher resolution in cryo-EM by the combination of macromolecular prior knowledge and image-processing tools.

Authors:  Erney Ramírez-Aportela; Jose M Carazo; Carlos Oscar S Sorzano
Journal:  IUCrJ       Date:  2022-08-03       Impact factor: 5.588

7.  Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures.

Authors:  Roberto Melero; Carlos Oscar S Sorzano; Brent Foster; José-Luis Vilas; Marta Martínez; Roberto Marabini; Erney Ramírez-Aportela; Ruben Sanchez-Garcia; David Herreros; Laura Del Caño; Patricia Losana; Yunior C Fonseca-Reyna; Pablo Conesa; Daniel Wrapp; Pablo Chacon; Jason S McLellan; Hemant D Tagare; Jose-Maria Carazo
Journal:  bioRxiv       Date:  2020-07-08

8.  Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium.

Authors:  Dmitry A Semchonok; Jyotirmoy Mondal; Connor J Cooper; Katrina Schlum; Meng Li; Muhamed Amin; Carlos O S Sorzano; Erney Ramírez-Aportela; Panagiotis L Kastritis; Egbert J Boekema; Albert Guskov; Barry D Bruce
Journal:  Plant Commun       Date:  2021-10-13
  8 in total

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