Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy

JM De la Rosa-Trevin, A Quintana, L Del Cano… - Journal of structural …, 2016 - Elsevier
In the past few years, 3D electron microscopy (3DEM) has undergone a revolution in
instrumentation and methodology. One of the central players in this wide-reaching change is …

Single-particle refinement and variability analysis in EMAN2. 1

SJ Ludtke - Methods in enzymology, 2016 - Elsevier
CryoEM single-particle reconstruction has been growing rapidly over the last 3 years largely
due to the development of direct electron detectors, which have provided data with dramatic …

emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging

BA Himes, P Zhang - Nature methods, 2018 - nature.com
Macromolecular complexes are intrinsically flexible and often challenging to purify for
structure determination by single-particle cryo-electron microscopy (cryo-EM). Such …

[PDF][PDF] A pipeline approach to single-particle processing in RELION

R Fernandez-Leiro, SHW Scheres - Acta Crystallographica Section …, 2017 - journals.iucr.org
The formal concept of a workflow to single-particle analysis of cryo-electron microscopy
(cryo-EM) images in the RELION program is described. In this approach, the structure …

Databases and archiving for CryoEM

A Patwardhan, CL Lawson - Methods in enzymology, 2016 - Elsevier
CryoEM in structural biology is currently served by three public archives—EMDB for 3DEM
reconstructions, PDB for models built from 3DEM reconstructions, and EMPIAR for the raw …

[PDF][PDF] Community recommendations on cryoEM data archiving and validation

GJ Kleywegt, PD Adams, SJ Butcher, CL Lawson… - IUCrJ, 2024 - journals.iucr.org
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data
requirements for the deposition and validation of cryoEM structures, with a focus on single …

An atypical BRCT–BRCT interaction with the XRCC1 scaffold protein compacts human DNA ligase IIIα within a flexible DNA repair complex

M Hammel, I Rashid, A Sverzhinsky… - Nucleic acids …, 2021 - academic.oup.com
Abstract The XRCC1–DNA ligase IIIα complex (XL) is critical for DNA single-strand break
repair, a key target for PARP inhibitors in cancer cells deficient in homologous …

[HTML][HTML] Evolving data standards for cryo-EM structures

CL Lawson, HM Berman, W Chiu - Structural Dynamics, 2020 - pubs.aip.org
Electron cryo-microscopy (cryo-EM) is increasingly being used to determine 3D structures of
a broad spectrum of biological specimens from molecules to cells. Anticipating this progress …

Advances in image processing for single-particle analysis by electron cryomicroscopy and challenges ahead

JL Vilas, N Tabassum, J Mota, D Maluenda… - Current Opinion in …, 2018 - Elsevier
Electron cryomicroscopy (cryoEM) is essential for the study and functional understanding of
non-crystalline macromolecules such as proteins. These molecules cannot be imaged using …

ACE-HetEM for ab initio heterogenous cryo-EM 3D reconstruction

W Chen, L Yao, Z Xia, Y Wang - arXiv preprint arXiv:2308.04956, 2023 - arxiv.org
Due to the extremely low signal-to-noise ratio (SNR) and unknown poses (projection angles
and image translation) in cryo-EM experiments, reconstructing 3D structures from 2D images …