Journal ArticleDOI
SIMPLE: Software for ab initio reconstruction of heterogeneous single-particles
Dominika Elmlund,Hans Elmlund +1 more
TLDR
The open source software suite SIMPLE: Single-particle IMage Processing Linux Engine provides data analysis methods for single-particles cryo-electron microscopy by addressing the problem of obtaining 3D reconstructions from 2D projections only, without using an input reference volume for approximating orientations.About:
This article is published in Journal of Structural Biology.The article was published on 2012-12-01. It has received 87 citations till now. The article focuses on the topics: Projection (set theory) & Reconstruction algorithm.read more
Citations
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Journal ArticleDOI
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
TL;DR: It is shown that stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms permit the major steps in cryo-EM structure determination to be performed in hours or minutes on an inexpensive desktop computer.
Journal ArticleDOI
Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2
TL;DR: An implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow, and it is shown that the use of single precision arithmetic does not adversely affect results.
Journal ArticleDOI
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.
Journal ArticleDOI
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.
Journal ArticleDOI
Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy.
J.M. de la Rosa-Trevín,A. Quintana,L. del Cano,A. Zaldívar,I. Foche,J. Gutiérrez,Josué Gómez-Blanco,Jordi Burguet-Castell,J. Cuenca-Alba,Vahid Abrishami,Javier Vargas,Joaquín Otón,Grigory Sharov,José Luis Vilas,J. Navas,P. Conesa,Mohsen Kazemi,Roberto Marabini,Carlos Oscar S. Sorzano,Carlos Oscar S. Sorzano,José María Carazo +20 more
TL;DR: Scipion is a software framework for integrating several 3DEM software packages through a workflow-based approach that allows the execution of reusable, standardized, traceable and reproducible image-processing protocols.
References
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Journal ArticleDOI
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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LIII. On lines and planes of closest fit to systems of points in space
TL;DR: This paper is concerned with the construction of planes of closest fit to systems of points in space and the relationships between these planes and the planes themselves.
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The Design and Implementation of FFTW3
Matteo Frigo,Steven G. Johnson +1 more
TL;DR: It is shown that such an approach can yield an implementation of the discrete Fourier transform that is competitive with hand-optimized libraries, and the software structure that makes the current FFTW3 version flexible and adaptive is described.
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Probabilistic Principal Component Analysis
TL;DR: In this paper, the principal axes of a set of observed data vectors may be determined through maximum-likelihood estimation of parameters in a latent variable model closely related to factor analysis.