Likelihood-based classification of cryo-EM images using FREALIGN.
TLDR
An implementation of maximum likelihood classification for single particle electron cryo-microscopy that is based on the FREALIGN software yields performance on par with other maximum likelihood implementations, while remaining computationally efficient.About:
This article is published in Journal of Structural Biology.The article was published on 2013-09-01 and is currently open access. It has received 267 citations till now. The article focuses on the topics: Expectation–maximization algorithm & Marginal likelihood.read more
Citations
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cisTEM, user-friendly software for single-particle image processing
TL;DR: New open-source software called cisTEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging is developed, optimized to enable processing of typical datasets on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing.
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How cryo-EM is revolutionizing structural biology
TL;DR: The recent advances in electron detection and image processing are reviewed and the exciting new opportunities that they offer to structural biology research are illustrated.
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Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6
Tim Grant,Nikolaus Grigorieff +1 more
TL;DR: A method of using optimal exposure values to filter movie frames, yielding images with improved contrast that lead to higher resolution reconstructions that should benefit cryo-EM work on all types of samples, especially those of relatively low-molecular mass.
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Addressing Preferred Specimen Orientation in Single-Particle Cryo-EM through Tilting
Yong Zi Tan,Philip R. Baldwin,Joseph H. Davis,James R. Williamson,Clinton S. Potter,Bridget Carragher,Dmitry Lyumkis +6 more
TL;DR: These methods were applied to determine the structures at near-atomic resolution of the influenza hemagglutinin trimer, which adopts a highly preferred specimen orientation, and of ribosomal biogenesis intermediates, which adopt moderately preferred orientations.
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A primer to single-particle cryo-electron microscopy.
TL;DR: This primer explains the different steps and considerations involved in structure determination by single-particle cryo-EM to provide an overview for scientists wishing to understand more about this technique and the interpretation of data obtained with it, as well as a starting guide for new practitioners.
References
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UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F. Pettersen,Thomas D. Goddard,Conrad C. Huang,Gregory S. Couch,Daniel M. Greenblatt,Elaine C. Meng,Thomas E. Ferrin +6 more
TL;DR: Two unusual extensions are presented: Multiscale, which adds the ability to visualize large‐scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales.
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RELION: implementation of a Bayesian approach to cryo-EM structure determination.
TL;DR: Developments that reduce the computational costs of the underlying maximum a posteriori (MAP) algorithm, as well as statistical considerations that yield new insights into the accuracy with which the relative orientations of individual particles may be determined are described.
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EMAN: semiautomated software for high-resolution single-particle reconstructions.
TL;DR: EMAN (Electron Micrograph ANalysis), a software package for performing semiautomated single-particle reconstructions from transmission electron micrographs, was written from scratch in C++ and is provided free of charge on the Web site.
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Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy.
TL;DR: The hand determination and refinement optimization procedure is applied to image pairs of the dihydrolipoyl acetyltransferase (E2) catalytic core of the pyruvate dehydrogenase complex from Bacillus stearothermophilus taken by low-dose electron cryomicroscopy.
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Accurate determination of local defocus and specimen tilt in electron microscopy
TL;DR: Two computer programs are presented, CTFFIND3 and CTFTILT, which determine defocus parameters from images of untilted specimens, as well as defocus and tilt parameters from image of tilted specimens, respectively, using a simple algorithm.