The critical node detection problem in networks: A survey

M Lalou, MA Tahraoui, H Kheddouci - Computer Science Review, 2018 - Elsevier
In networks, not all nodes have the same importance, and some are more important than
others. The issue of finding the most important nodes in networks has been addressed …

[HTML][HTML] Stapled peptides inhibitors: a new window for target drug discovery

AM Ali, J Atmaj, N Van Oosterwijk, MR Groves… - Computational and …, 2019 - Elsevier
Protein-protein interaction (PPI) is a hot topic in clinical research as protein networking has a
major impact in human disease. Such PPIs are potential drugs targets, leading to the need …

Protein interface prediction using graph convolutional networks

A Fout, J Byrd, B Shariat… - Advances in neural …, 2017 - proceedings.neurips.cc
We consider the prediction of interfaces between proteins, a challenging problem with
important applications in drug discovery and design, and examine the performance of …

Conditional antibody design as 3d equivariant graph translation

X Kong, W Huang, Y Liu - arXiv preprint arXiv:2208.06073, 2022 - arxiv.org
Antibody design is valuable for therapeutic usage and biological research. Existing deep-
learning-based methods encounter several key issues: 1) incomplete context for …

Targeting undruggable transcription factors with PROTACs: advances and perspectives

Y Li, J Song, P Zhou, J Zhou, S Xie - Journal of Medicinal …, 2022 - ACS Publications
Dysregulation of transcription factors has been implicated in a variety of human diseases.
However, these proteins have traditionally been regarded as undruggable and only a …

Evolution of in silico strategies for protein-protein interaction drug discovery

SJY Macalino, S Basith, NAB Clavio, H Chang, S Kang… - Molecules, 2018 - mdpi.com
The advent of advanced molecular modeling software, big data analytics, and high-speed
processing units has led to the exponential evolution of modern drug discovery and better …

[HTML][HTML] Targeting protein–protein interactions, a wide open field for drug design

M Bakail, F Ochsenbein - Comptes …, 2016 - comptes-rendus.academie-sciences …
Targeting protein–protein interactions has long been considered as a very difficult if
impossible task, but over the past decade, front lines have moved. The number of successful …

DNA–protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or …

KA Wilson, JL Kellie, SD Wetmore - Nucleic acids research, 2014 - academic.oup.com
Four hundred twenty-eight high-resolution DNA–protein complexes were chosen for a
bioinformatics study. Although 164 crystal structures (38% of those searched) contained no …

[HTML][HTML] Computational prediction of protein aggregation: Advances in proteomics, conformation-specific algorithms and biotechnological applications

J Santos, J Pujols, I Pallarès, V Iglesias… - Computational and …, 2020 - Elsevier
Protein aggregation is a widespread phenomenon that stems from the establishment of non-
native intermolecular contacts resulting in protein precipitation. Despite its deleterious …

Membrane transporter dimerization driven by differential lipid solvation energetics of dissociated and associated states

R Chadda, N Bernhardt, EG Kelley, SCM Teixeira… - Elife, 2021 - elifesciences.org
Over two-thirds of integral membrane proteins of known structure assemble into oligomers.
Yet, the forces that drive the association of these proteins remain to be delineated, as the …