[PDF][PDF] Phaser. MRage: automated molecular replacement

G Bunkóczi, N Echols, AJ McCoy… - … Section D: Biological …, 2013 - journals.iucr.org
Phaser. MRage is a molecular-replacement automation framework that implements a full
model-generation workflow and provides several layers of model exploration to the user. It is …

Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination

A Wlodawer, W Minor, Z Dauter… - The FEBS journal, 2013 - Wiley Online Library
The number of macromolecular structures deposited in the Protein Data Bank now
approaches 100 000, with the vast majority of them determined by crystallographic methods …

[PDF][PDF] CCP4i2: the new graphical user interface to the CCP4 program suite

L Potterton, J Agirre, C Ballard, K Cowtan… - … Section D: Structural …, 2018 - journals.iucr.org
The CCP4 (Collaborative Computational Project, Number 4) software suite for
macromolecular structure determination by X-ray crystallography groups brings together …

Molecular replacement with MOLREP

A Vagin, A Teplyakov - Acta Crystallographica Section D: Biological …, 2010 - journals.iucr.org
MOLREP is an automated program for molecular replacement that utilizes a number of
original approaches to rotational and translational search and data preparation. Since the …

[PDF][PDF] BALBES: a molecular-replacement pipeline

F Long, AA Vagin, P Young… - … Section D: Biological …, 2008 - journals.iucr.org
The number of macromolecular structures solved and deposited in the Protein Data Bank
(PDB) is higher than 40 000. Using this information in macromolecular crystallography (MX) …

Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gut

A Bell, J Brunt, E Crost, L Vaux, R Nepravishta… - Nature …, 2019 - nature.com
Sialic acid (N-acetylneuraminic acid (Neu5Ac)) is commonly found in the terminal location of
colonic mucin glycans where it is a much-coveted nutrient for gut bacteria, including …

Efficient O-glycosylation of triterpenes enabled by protein engineering of plant glycosyltransferase UGT74AC1

J Li, J Yang, S Mu, N Shang, C Liu, Y Zhu, Y Cai… - ACS …, 2020 - ACS Publications
Triterpene O-glycosylation has attracted significant interest from the pharmaceutical industry
as a valuable means for drug design and development. Plant glycosyltransferases, which …

AlphaFold two years on: Validation and impact

O Kovalevskiy, J Mateos-Garcia… - Proceedings of the …, 2024 - pnas.org
Two years on from the initial release of AlphaFold, we have seen its widespread adoption as
a structure prediction tool. Here, we discuss some of the latest work based on AlphaFold …

Diverse specificity and effector function among human antibodies to HIV-1 envelope glycoprotein epitopes exposed by CD4 binding

Y Guan, M Pazgier, MM Sajadi… - Proceedings of the …, 2013 - National Acad Sciences
The HIV-1 envelope glycoprotein (Env) undergoes conformational transitions consequent to
CD4 binding and coreceptor engagement during viral entry. The physical steps in this …

Activation of PARP2/ARTD2 by DNA damage induces conformational changes relieving enzyme autoinhibition

E Obaji, MM Maksimainen, A Galera-Prat… - Nature …, 2021 - nature.com
Human PARP2/ARTD2 is an ADP-ribosyltransferase which, when activated by 5′-
phosphorylated DNA ends, catalyses poly-ADP-ribosylation of itself, other proteins and …