Challenges and opportunities in cryo-EM single-particle analysis

D Lyumkis - Journal of Biological Chemistry, 2019 - ASBMB
Cryogenic electron microscopy (cryo-EM) enables structure determination of
macromolecular objects and their assemblies. Although the techniques have been …

[HTML][HTML] Cryo-electron microscopy for structural analysis of dynamic biological macromolecules

K Murata, M Wolf - Biochimica et Biophysica Acta (BBA)-General Subjects, 2018 - Elsevier
Background Since the introduction of what became today's standard for cryo-embedding of
biological macromolecules at native conditions more than 30 years ago, techniques and …

New tools for automated cryo-EM single-particle analysis in RELION-4.0

D Kimanius, L Dong, G Sharov, T Nakane… - Biochemical …, 2021 - portlandpress.com
We describe new tools for the processing of electron cryo-microscopy (cryo-EM) images in
the fourth major release of the RELION software. In particular, we introduce VDAM, a …

EMPIAR: the electron microscopy public image archive

A Iudin, PK Korir, S Somasundharam… - Nucleic Acids …, 2023 - academic.oup.com
Public archiving in structural biology is well established with the Protein Data Bank (PDB;
wwPDB. org) catering for atomic models and the Electron Microscopy Data Bank (EMDB; …

New tools for automated high-resolution cryo-EM structure determination in RELION-3

J Zivanov, T Nakane, BO Forsberg, D Kimanius… - elife, 2018 - elifesciences.org
Here, we describe the third major release of RELION. CPU-based vector acceleration has
been added in addition to GPU support, which provides flexibility in use of resources and …

Structure of hepcidin-bound ferroportin reveals iron homeostatic mechanisms

CB Billesbølle, CM Azumaya, RC Kretsch, AS Powers… - Nature, 2020 - nature.com
The serum level of iron in humans is tightly controlled by the action of the hormone hepcidin
on the iron efflux transporter ferroportin. Hepcidin regulates iron absorption and recycling by …

nextPYP: a comprehensive and scalable platform for characterizing protein variability in situ using single-particle cryo-electron tomography

HF Liu, Y Zhou, Q Huang, J Piland, W Jin, J Mandel… - Nature …, 2023 - nature.com
Single-particle cryo-electron tomography is an emerging technique capable of determining
the structure of proteins imaged within the native context of cells at molecular resolution …

SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM

T Wagner, F Merino, M Stabrin, T Moriya… - Communications …, 2019 - nature.com
Selecting particles from digital micrographs is an essential step in single-particle electron
cryomicroscopy (cryo-EM). As manual selection of complete datasets—typically comprising …

Real-time cryo-electron microscopy data preprocessing with Warp

D Tegunov, P Cramer - Nature methods, 2019 - nature.com
The acquisition of cryo-electron microscopy (cryo-EM) data from biological specimens must
be tightly coupled to data preprocessing to ensure the best data quality and microscope …

Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs

T Bepler, A Morin, M Rapp, J Brasch, L Shapiro… - Nature …, 2019 - nature.com
Cryo-electron microscopy is a popular method for the determination of protein structures;
however, identifying a sufficient number of particles for analysis can take months of manual …