Journal ArticleDOI
Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy.
TLDR
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.About:
This article is published in Journal of Molecular Biology.The article was published on 2003-10-31. It has received 1959 citations till now. The article focuses on the topics: Tilt (optics).read more
Citations
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Journal ArticleDOI
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.
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
Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2.
TL;DR: Cryo–electron microscopy structures of full-length human ACE2 in the presence of the neutral amino acid transporter B0AT1 with or without the receptor binding domain (RBD) of the surface spike glycoprotein of SARS-CoV-2 are presented, providing important insights into the molecular basis for coronavirus recognition and infection.
Journal ArticleDOI
How good are my data and what is the resolution
TL;DR: The new scaling program AIMLESS is described and tests of refinements at different resolutions are compared with analyses from the scaling step.
Journal ArticleDOI
New tools for automated high-resolution cryo-EM structure determination in RELION-3.
Jasenko Zivanov,Takanori Nakane,Björn O. Forsberg,Dari Kimanius,Wim J. H. Hagen,Erik Lindahl,Erik Lindahl,Sjors H.W. Scheres +7 more
TL;DR: CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations in the third major release of RELION.
References
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Journal ArticleDOI
The CCP4 suite: programs for protein crystallography
TL;DR: The CCP4 (Collaborative Computational Project, number 4) program suite is a collection of programs and associated data and subroutine libraries which can be used for macromolecular structure determination by X-ray crystallography.
Journal ArticleDOI
Improved methods for building protein models in electron density maps and the location of errors in these models.
TL;DR: In this paper, the authors describe strategies and tools that help to alleviate this problem and simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in peptide and side-chain conformations.
Journal ArticleDOI
Small‐Angle Scattering of X‐Rays
Journal ArticleDOI
CRYSOL : a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates
TL;DR: In this paper, a program for evaluating the solution scattering from macromolecules with known atomic structure is presented, which uses multipole expansion for fast calculation of the spherically averaged scattering pattern and takes into account the hydration shell.
MonographDOI
Three-Dimensional Electron Microscopy of Macromolecular Assemblies
TL;DR: In this article, a three-dimensional reconstruction interpretation of 3D images of macromolecules is presented. Butts et al. reconstructed macromoles from micrographs of single macromolcules.