FREALIGN: high-resolution refinement of single particle structures.

By N. Grigorieff. Journal of Structural Biology, 2007

536 citations recorded by the source corpus.

Subfields: Molecular Biology, Structural Biology, Surfaces, Coatings and Films

View Paper: https://www.semanticscholar.org/paper/55257ac01aed277506a3e55d6c9a7ec4557c3086

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Citations in the corpus

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy (2013, methodology): “Stacks of particles were picked by hand using Ximdisp [50], CTF estimated using CTFFIND3 [51], boxed particle densities floated and normalised using BOXIMAGE [52], and 3D maps calculated using Frealign [9], Relion [10], Xmipp [53,54] and a new program still under development by McMullan (unpublished”
Gctf: Real-time CTF determination and correction (2015, methodology): “For typical usage (box size 512 pixels and search step 500Å), Gctf can process more than 1000 micrographs in the time CTFFIND3 requires to process one.”
Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2 (2016, unknown): “, 2007), frealign (Grigorieff, 2007), xmipp (Scheres et al.”
Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM (2018, methodology): “Reconstructions are typically performed in Fourier space using the projection-slice theorem, as for example in RELION (Scheres, 2012) and Frealign (Grigorieff, 2007), before the reconstructed maps are subsequently calculated in real space.”
Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction (2019, methodology): “In the standard cryo-EM 3D reconstruction problem set up [12, 22, 26], a generative model describes the formation of images of a target protein in an electron microscope.”
cisTEM: User-friendly software for single-particle image processing (2017, methodology): “17 Score-based weighting In previous versions of Frealign, resolution-dependent weighting was 344 applied to the particle images during reconstruction (the Frealign parameter was called “PBC”, 345 (Grigorieff, 2007)).”
A Bayesian View on Cryo-EM Structure Determination (2012, methodology): “XMIPP uses a constant for the SNR term in the Wiener filter and sets its value in the same way as FREALIGN does.(26) As also mentioned above, a single value is, however, inadequate to describe the intrinsic 3D behavior of the SNR in Fourier space.”
High resolution microtubule structures reveal the structural transitions in αβ–tubulin upon GTP hydrolysis (2014, methodology): “A final refinement of the alignment parameters was performed only for the 14 pf MT particles using FREALIGN (Grigorieff, 2007), with a modified script that incorporated the symmetrization and MT seam regeneration after each round.”
A Primer to Single-Particle Cryo-Electron Microscopy (2015, unknown): “, 2013) using RELION (Scheres, 2012) and FREALIGN (Grigorieff, 2007; Lyumkis et al., 2013) produces virtually identical features in the well-defined density regions within the transmembrane domain (Figure 4A-D).”
3D Variability Analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM (2020, methodology): “Under the standard cryo-EM image formation model (Frank, 2007; Grigorieff, 2007; Punjani et al., 2017; Scheres, 2012a), a 2D particle image, Xi, is a corrupted projection of the target 3D density V from an unobserved pose φi, plus additive noise, η.”