[PDF][PDF] Recent developments in the CCP-EM software suite

T Burnley, CM Palmer, M Winn - Acta Crystallographica Section D …, 2017 - journals.iucr.org
As part of its remit to provide computational support to the cryo-EM community, the
Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) has produced …

Cryo-EM in molecular and cellular biology

HR Saibil - Molecular Cell, 2022 - cell.com
This review summarizes the current state of methods and results achievable by cryo-electron
microscopy (cryo-EM) imaging for molecular, cell, and structural biologists who wish to …

[PDF][PDF] ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

TI Croll - Acta Crystallographica Section D: Structural Biology, 2018 - journals.iucr.org
This paper introduces ISOLDE, a new software package designed to provide an intuitive
environment for high-fidelity interactive remodelling/refinement of macromolecular models …

Measurement of atom resolvability in cryo-EM maps with Q-scores

G Pintilie, K Zhang, Z Su, S Li, MF Schmid, W Chiu - Nature methods, 2020 - nature.com
Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of
individual atoms can be achieved. However, resolvability is not necessarily uniform …

[PDF][PDF] Automated map sharpening by maximization of detail and connectivity

TC Terwilliger, OV Sobolev, PV Afonine… - … Section D: Structural …, 2018 - journals.iucr.org
An algorithm for automatic map sharpening is presented that is based on optimization of the
detail and connectivity of the sharpened map. The detail in the map is reflected in the …

Model-based local density sharpening of cryo-EM maps

AJ Jakobi, M Wilmanns, C Sachse - Elife, 2017 - elifesciences.org
Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM
structure determination process. Here, we introduce a general procedure for local …

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

CL Lawson, A Kryshtafovych, PD Adams, PV Afonine… - Nature …, 2021 - nature.com
This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to
(1) assess the quality of models that can be produced from cryogenic electron microscopy …

CR-I-TASSER: assemble protein structures from cryo-EM density maps using deep convolutional neural networks

X Zhang, B Zhang, PL Freddolino, Y Zhang - Nature methods, 2022 - nature.com
Cryo-electron microscopy (cryo-EM) has become a leading approach for protein structure
determination, but it remains challenging to accurately model atomic structures with cryo-EM …

Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase

C Deville, M Carroni, KB Franke, M Topf, B Bukau… - Science …, 2017 - science.org
Refolding aggregated proteins is essential in combating cellular proteotoxic stress. Together
with Hsp70, Hsp100 chaperones, including Escherichia coli ClpB, form a powerful …

Cryo-EM structure and B-factor refinement with ensemble representation

JG Beton, T Mulvaney, T Cragnolini, M Topf - Nature Communications, 2024 - nature.com
Cryo-EM experiments produce images of macromolecular assemblies that are combined to
produce three-dimensional density maps. Typically, atomic models of the constituent …