[HTML][HTML] Exploring the IRE1 interactome: from canonical signaling functions to unexpected roles

S Le Goupil, H Laprade, M Aubry, E Chevet - Journal of Biological …, 2024‏ - Elsevier
The unfolded protein response (UPR) is a mechanism aiming at restoring endoplasmic
reticulum (ER) homeostasis and is likely involved in other adaptive pathways. The UPR is …

Network medicine framework for identifying drug-repurposing opportunities for COVID-19

D Morselli Gysi, Í Do Valle, M Zitnik, A Ameli… - Proceedings of the …, 2021‏ - pnas.org
The COVID-19 pandemic has highlighted the need to quickly and reliably prioritize clinically
approved compounds for their potential effectiveness for severe acute respiratory syndrome …

The social and structural architecture of the yeast protein interactome

AC Michaelis, AD Brunner, M Zwiebel, F Meier… - Nature, 2023‏ - nature.com
Cellular functions are mediated by protein–protein interactions, and map** the
interactome provides fundamental insights into biological systems. Affinity purification …

From classical to new generation approaches: An excursus of-omics methods for investigation of protein-protein interaction networks

I Iacobucci, V Monaco, F Cozzolino, M Monti - Journal of Proteomics, 2021‏ - Elsevier
Functional Proteomics aims to the identification of in vivo protein-protein interaction (PPI) in
order to piece together protein complexes, and therefore, cell pathways involved in …

Cross-linking mass spectrometry discovers, evaluates, and corroborates structures and protein–protein interactions in the human cell

TK Bartolec, X Vázquez-Campos, A Norman… - Proceedings of the …, 2023‏ - pnas.org
Significant recent advances in structural biology, particularly in the field of cryoelectron
microscopy, have dramatically expanded our ability to create structural models of proteins …

Transforming the language of life: transformer neural networks for protein prediction tasks

A Nambiar, M Heflin, S Liu, S Maslov… - Proceedings of the 11th …, 2020‏ - dl.acm.org
The scientific community is rapidly generating protein sequence information, but only a
fraction of these proteins can be experimentally characterized. While promising deep …

IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis

M Kotlyar, C Pastrello, Z Ahmed, J Chee… - Nucleic Acids …, 2022‏ - academic.oup.com
Improved bioassays have significantly increased the rate of identifying new protein-protein
interactions (PPIs), and the number of detected human PPIs has greatly exceeded early …

Drugst. One—a plug-and-play solution for online systems medicine and network-based drug repurposing

A Maier, M Hartung, M Abovsky… - Nucleic Acids …, 2024‏ - academic.oup.com
In recent decades, the development of new drugs has become increasingly expensive and
inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly …

PrePPI: a structure informed proteome-wide database of protein–protein interactions

D Petrey, H Zhao, SJ Trudeau, D Murray… - Journal of molecular …, 2023‏ - Elsevier
We present an updated version of the Predicting Protein-Protein Interactions (PrePPI)
webserver which predicts PPIs on a proteome-wide scale. PrePPI combines structural and …

Noncoding RNAs improve the predictive power of network medicine

D Morselli Gysi, AL Barabasi - Proceedings of the National Academy of …, 2023‏ - pnas.org
Network medicine has improved the mechanistic understanding of disease, offering
quantitative insights into disease mechanisms, comorbidities, and novel diagnostic tools and …