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Literature DB >> 24607413

Automated particle picking for low-contrast macromolecules in cryo-electron microscopy.

Robert Langlois¹, Jesper Pallesen², Jordan T Ash³, Danny Nam Ho⁴, John L Rubinstein⁵, Joachim Frank⁶.

Abstract

Cryo-electron microscopy is an increasingly popular tool for studying the structure and dynamics of biological macromolecules at high resolution. A crucial step in automating single-particle reconstruction of a biological sample is the selection of particle images from a micrograph. We present a novel algorithm for selecting particle images in low-contrast conditions; it proves more effective than the human eye on close-to-focus micrographs, yielding improved or comparable resolution in reconstructions of two macromolecular complexes.

Entities: Chemical

Keywords: Automation; Cryo-EM; High-resolution; Machine-learning; Particle selection

Mesh：

Substances：

Year: 2014 PMID： 24607413 PMCID： PMC4063204 DOI： 10.1016/j.jsb.2014.03.001

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

22 in total

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

Authors: Peter B Rosenthal; Richard Henderson
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2. Accurate determination of local defocus and specimen tilt in electron microscopy.

Authors: Joseph A Mindell; Nikolaus Grigorieff
Journal: J Struct Biol Date: 2003-06 Impact factor: 2.867

3. Fast automatic particle picking from cryo-electron micrographs using a locally normalized cross-correlation function: a case study.

Authors: B K Rath; J Frank
Journal: J Struct Biol Date: 2004 Jan-Feb Impact factor: 2.867

4. SIGNATURE: a single-particle selection system for molecular electron microscopy.

Authors: James Z Chen; Nikolaus Grigorieff
Journal: J Struct Biol Date: 2006-06-17 Impact factor: 2.867

5. EMAN2: an extensible image processing suite for electron microscopy.

Authors: Guang Tang; Liwei Peng; Philip R Baldwin; Deepinder S Mann; Wen Jiang; Ian Rees; Steven J Ludtke
Journal: J Struct Biol Date: 2006-06-08 Impact factor: 2.867

6. Experimental evaluation of support vector machine-based and correlation-based approaches to automatic particle selection.

Authors: Pablo Arbeláez; Bong-Gyoon Han; Dieter Typke; Joseph Lim; Robert M Glaeser; Jitendra Malik
Journal: J Struct Biol Date: 2011-05-25 Impact factor: 2.867

7. A clarification of the terms used in comparing semi-automated particle selection algorithms in cryo-EM.

Authors: Robert Langlois; Joachim Frank
Journal: J Struct Biol Date: 2011-03-21 Impact factor: 2.867

8. TMaCS: a hybrid template matching and classification system for partially-automated particle selection.

Authors: Jianhua Zhao; Marcus A Brubaker; John L Rubinstein
Journal: J Struct Biol Date: 2013-01-16 Impact factor: 2.867

9. Reference-free particle selection enhanced with semi-supervised machine learning for cryo-electron microscopy.

Authors: Robert Langlois; Jesper Pallesen; Joachim Frank
Journal: J Struct Biol Date: 2011-06-17 Impact factor: 2.867

10. RELION: implementation of a Bayesian approach to cryo-EM structure determination.

Authors: Sjors H W Scheres
Journal: J Struct Biol Date: 2012-09-19 Impact factor: 2.867

21 in total

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Authors: Zheng Liu; Cristina Gutierrez-Vargas; Jia Wei; Robert A Grassucci; Madhumitha Ramesh; Noel Espina; Ming Sun; Beril Tutuncuoglu; Susan Madison-Antenucci; John L Woolford; Liang Tong; Joachim Frank
Journal: Proc Natl Acad Sci U S A Date: 2016-10-10 Impact factor: 11.205

2. APPLE picker: Automatic particle picking, a low-effort cryo-EM framework.

Authors: Ayelet Heimowitz; Joakim Andén; Amit Singer
Journal: J Struct Biol Date: 2018-08-19 Impact factor: 2.867

Review 3. 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

4. Critical Role for Saccharomyces cerevisiae Asc1p in Translational Initiation at Elevated Temperatures.

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Journal: Proteomics Date: 2018-10-23 Impact factor: 3.984

Review 5. 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

6. Efficient estimation of three-dimensional covariance and its application in the analysis of heterogeneous samples in cryo-electron microscopy.

Authors: Hstau Y Liao; Yaser Hashem; Joachim Frank
Journal: Structure Date: 2015-05-14 Impact factor: 5.006

7. Structural dynamics of ribosome subunit association studied by mixing-spraying time-resolved cryogenic electron microscopy.

Authors: Bo Chen; Sandip Kaledhonkar; Ming Sun; Bingxin Shen; Zonghuan Lu; David Barnard; Toh-Ming Lu; Ruben L Gonzalez; Joachim Frank
Journal: Structure Date: 2015-05-21 Impact factor: 5.006