[PDF][PDF] Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

D Liebschner, PV Afonine, ML Baker… - … Section D: Structural …, 2019 - journals.iucr.org
Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods
to determine three-dimensional macromolecular structures, which are required to …

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 …

MolProbity: more and better reference data for improved all‐atom structure validation

CJ Williams, JJ Headd, NW Moriarty… - Protein …, 2018 - Wiley Online Library
This paper describes the current update on macromolecular model validation services that
are provided at the MolProbity website, emphasizing changes and additions since the …

A global Ramachandran score identifies protein structures with unlikely stereochemistry

OV Sobolev, PV Afonine, NW Moriarty, ML Hekkelman… - Structure, 2020 - cell.com
Ramachandran plots report the distribution of the (ϕ, ψ) torsion angles of the protein
backbone and are one of the best quality metrics of experimental structure models. Typically …

Atg18 oligomer organization in assembled tubes and on lipid membrane scaffolds

D Mann, SA Fromm, A Martinez-Sanchez… - Nature …, 2023 - nature.com
Abstract Autophagy-related protein 18 (Atg18) participates in the elongation of early
autophagosomal structures in concert with Atg2 and Atg9 complexes. How Atg18 contributes …

[PDF][PDF] Dose-resolved serial synchrotron and XFEL structures of radiation-sensitive metalloproteins

A Ebrahim, T Moreno-Chicano, MV Appleby… - IUCrJ, 2019 - journals.iucr.org
An approach is demonstrated to obtain, in a sample-and time-efficient manner, multiple dose-
resolved crystal structures from room-temperature protein microcrystals using identical fixed …

New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink “waters,” and NGL Viewer to recapture online 3D graphics

MG Prisant, CJ Williams, VB Chen… - Protein …, 2020 - Wiley Online Library
The MolProbity web service provides macromolecular model validation to help correct local
errors, for the structural biology community worldwide. Here we highlight new validation …

Structural principles of SNARE complex recognition by the AAA+ protein NSF

KI White, M Zhao, UB Choi, RA Pfuetzner, AT Brunger - Elife, 2018 - elifesciences.org
The recycling of SNARE proteins following complex formation and membrane fusion is an
essential process in eukaryotic trafficking. A highly conserved AAA+ protein, NSF (N …

Modelling structures in cryo-EM maps

S Malhotra, S Träger, M Dal Peraro, M Topf - Current Opinion in Structural …, 2019 - Elsevier
Highlights•Approaches to the structure determination and modelling of macromolecular
assemblies depend on the resolution of their cryo-EM map.•Insights into structure dynamics …

Integrating model simulation tools and cryo‐electron microscopy

JG Beton, T Cragnolini, M Kaleel… - Wiley …, 2023 - Wiley Online Library
The power of computer simulations, including machine‐learning, has become an
inseparable part of scientific analysis of biological data. This has significantly impacted the …