What method to use for protein–protein docking?

KA Porter, I Desta, D Kozakov, S Vajda - Current opinion in structural …, 2019 - Elsevier
Highlights•The best servers based on “free” docking methods find acceptable models
among the top 10 predictions for around 40% of the targets.•Re-ranking the predictions by a …

Solution NMR: A powerful tool for structural and functional studies of membrane proteins in reconstituted environments

R Puthenveetil, O Vinogradova - Journal of Biological Chemistry, 2019 - ASBMB
A third of the genes in prokaryotic and eukaryotic genomes encode membrane proteins that
are either essential for signal transduction and solute transport or function as scaffold …

HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA

G Weng, E Wang, Z Wang, H Liu, F Zhu… - Nucleic acids …, 2019 - academic.oup.com
Protein–protein interactions (PPIs) play an important role in the different functions of cells,
but accurate prediction of the three-dimensional structures for PPIs is still a notoriously …

Bispecific aptamer induced artificial protein-pairing: a strategy for selective inhibition of receptor function

L Wang, H Liang, J Sun, Y Liu, J Li, J Li… - Journal of the …, 2019 - ACS Publications
Cell surface receptors play a critical role in modulating intracellular signal transduction,
making them important drug targets. However, it remains challenging to develop a selective …

Mechanism of glucocerebrosidase activation and dysfunction in Gaucher disease unraveled by molecular dynamics and deep learning

R Romero, A Ramanathan, T Yuen… - Proceedings of the …, 2019 - National Acad Sciences
The lysosomal enzyme glucocerebrosidase-1 (GCase) catalyzes the cleavage of a major
glycolipid glucosylceramide into glucose and ceramide. The absence of fully functional …

c-Met activation leads to the establishment of a TGFβ-receptor regulatory network in bladder cancer progression

WJ Sim, PV Iyengar, D Lama, SKL Lui, HC Ng… - Nature …, 2019 - nature.com
Abstract Treatment of muscle-invasive bladder cancer remains a major clinical challenge.
Aberrant HGF/c-MET upregulation and activation is frequently observed in bladder cancer …

[PDF][PDF] COA6 is structurally tuned to function as a thiol-disulfide oxidoreductase in copper delivery to mitochondrial cytochrome c oxidase

S Soma, MN Morgada, MT Naik, A Boulet, AA Roesler… - Cell reports, 2019 - cell.com
In eukaryotes, cellular respiration is driven by mitochondrial cytochrome c oxidase (CcO), an
enzyme complex that requires copper cofactors for its catalytic activity. Insertion of copper …

Molecular docking and dynamic approach to virtual screen inhibitors against Esbp of Candidatus Liberibacter asiaticus

G Saini, V Dalal, BK Savita, N Sharma, P Kumar… - Journal of Molecular …, 2019 - Elsevier
Citrus greening (huanglongbing) is the most destructive disease of citrus worldwide caused
by Candidatus Liberibacter asiaticus (CLA). Currently, no strategies have been developed to …

HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures

J He, J Wang, H Tao, Y Xiao… - Nucleic Acids Research, 2019 - academic.oup.com
Interactions between nuclide acids (RNA/DNA) play important roles in many basic cellular
activities like transcription regulation, RNA processing, and protein synthesis. Therefore …

Phosphorylation of 14-3-3ζ links YAP transcriptional activation to hypoxic glycolysis for tumorigenesis

Y Jia, HY Li, J Wang, Y Wang, P Zhang, N Ma, SJ Mo - Oncogenesis, 2019 - nature.com
Hypoxic microenvironment deregulates metabolic homeostasis in cancer cells albeit the
underlying mechanisms involved in this process remain hitherto enigmatic. 14-3-3ζ/Yes …