Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

K Kappel, K Zhang, Z Su, AM Watkins, W Kladwang… - Nature …, 2020 - nature.com
The discovery and design of biologically important RNA molecules is outpacing three-
dimensional structural characterization. Here, we demonstrate that cryo-electron microscopy …

[HTML][HTML] Advances in methods for atomic resolution macromolecular structure determination

MC Thompson, TO Yeates, JA Rodriguez - F1000Research, 2020 - ncbi.nlm.nih.gov
Recent technical advances have dramatically increased the power and scope of structural
biology. New developments in high-resolution cryo-electron microscopy, serial X-ray …

Novel artificial intelligence-based approaches for ab initio structure determination and atomic model building for cryo-electron microscopy

MC DiIorio, AW Kulczyk - Micromachines, 2023 - mdpi.com
Single particle cryo-electron microscopy (cryo-EM) has emerged as the prevailing method
for near-atomic structure determination, shedding light on the important molecular …

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps

TC Terwilliger, PD Adams, PV Afonine, OV Sobolev - Nature methods, 2018 - nature.com
We report a fully automated procedure for the optimization and interpretation of
reconstructions from cryo-electron microscopy (cryo-EM) data, available in Phenix as …

Structural basis for ligand binding modes of CTP synthase

X Zhou, CJ Guo, CC Chang, J Zhong… - Proceedings of the …, 2021 - National Acad Sciences
Cytidine triphosphate synthase (CTPS), which comprises an ammonia ligase domain and a
glutamine amidotransferase domain, catalyzes the final step of de novo CTP biosynthesis …

Drosophila CTP synthase can form distinct substrate-and product-bound filaments

X Zhou, CJ Guo, HH Hu, J Zhong, Q Sun, D Liu… - Journal of Genetics and …, 2019 - Elsevier
Intracellular compartmentation is a key strategy for the functioning of a cell. In 2010, several
studies revealed that the metabolic enzyme CTP synthase (CTPS) can form filamentous …

De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes

K Kappel, S Liu, KP Larsen, G Skiniotis, EV Puglisi… - Nature …, 2018 - nature.com
Increasingly, cryo-electron microscopy (cryo-EM) is used to determine the structures of RNA–
protein assemblies, but nearly all maps determined with this method have biologically …

Simulation-based methods for model building and refinement in cryoelectron microscopy

T Dodd, C Yan, I Ivanov - Journal of Chemical Information and …, 2020 - ACS Publications
Advances in cryoelectron microscopy (cryo-EM) have revolutionized the structural
investigation of large macromolecular assemblies. In this review, we first provide a broad …

Cryo‐EM map interpretation and protein model‐building using iterative map segmentation

TC Terwilliger, PD Adams, PV Afonine… - Protein …, 2020 - Wiley Online Library
A procedure for building protein chains into maps produced by single‐particle electron cryo‐
microscopy (cryo‐EM) is described. The procedure is similar to the way an experienced …

EMBuilder: a template matching-based automatic model-building program for high-resolution cryo-electron microscopy maps

N Zhou, H Wang, J Wang - Scientific reports, 2017 - nature.com
The resolution of electron-potential maps in single-particle cryo-electron microscopy
(cryoEM) is approaching atomic or near-atomic resolution. However, no program currently …