[HTML][HTML] Unified alignment of protein-protein interaction networks

N Malod-Dognin, K Ban, N Pržulj - Scientific reports, 2017 - nature.com
Paralleling the increasing availability of protein-protein interaction (PPI) network data,
several network alignment methods have been proposed. Network alignments have been …

Biological relevance and therapeutic potential of the hypusine modification system

N Pällmann, M Braig, H Sievert, M Preukschas… - Journal of Biological …, 2015 - ASBMB
Hypusine modification of the eukaryotic initiation factor 5A (eIF-5A) is emerging as a crucial
regulator in cancer, infections, and inflammation. Although its contribution in translational …

Identification of crucial candidate genes and pathways in glioblastoma multiform by bioinformatics analysis

AM Alshabi, B Vastrad, IA Shaikh, C Vastrad - Biomolecules, 2019 - mdpi.com
The present study aimed to investigate the molecular mechanisms underlying glioblastoma
multiform (GBM) and its biomarkers. The differentially expressed genes (DEGs) were …

[HTML][HTML] Protein conformational switch discerned via network centrality properties

D Foutch, B Pham, T Shen - Computational and Structural Biotechnology …, 2021 - Elsevier
Network analysis has emerged as a powerful tool for examining structural biology systems.
The spatial organization of the components of a biomolecular structure has been rendered …

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study

JM Villaveces, RC Jimenez, P Porras, N del-Toro… - Database, 2015 - academic.oup.com
The evidence that two molecules interact in a living cell is often inferred from multiple
different experiments. Experimental data is captured in multiple repositories, but there is no …

Detecting protein complexes from signed protein-protein interaction networks

L Ou-Yang, DQ Dai, XF Zhang - IEEE/ACM transactions on …, 2015 - ieeexplore.ieee.org
Identification of protein complexes is fundamental for understanding the cellular functional
organization. With the accumulation of physical protein-protein interaction (PPI) data …

Genome-wide detection and analysis of multifunctional genes

Y Pritykin, D Ghersi, M Singh - PLoS computational biology, 2015 - journals.plos.org
Many genes can play a role in multiple biological processes or molecular functions.
Identifying multifunctional genes at the genome-wide level and studying their properties can …

Deep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis

T Zhou, S Wang, J Xu - BioRxiv, 2017 - biorxiv.org
Intra-protein residue-level contact prediction has drawn a lot of attentions in recent years
and made very good progress, but much fewer methods are dedicated to inter-protein …

Exploiting locational and topological overlap model to identify modules in protein interaction networks

L Cheng, P Liu, D Wang, KS Leung - BMC bioinformatics, 2019 - Springer
Background Clustering molecular network is a typical method in system biology, which is
effective in predicting protein complexes or functional modules. However, few studies have …

Presence and utility of intrinsically disordered regions in kinases

JJ Kathiriya, RR Pathak, E Clayman, B Xue… - Molecular …, 2014 - pubs.rsc.org
Since aberrant cell signaling pathways underlie majority of pathophysiological morbidities,
kinase inhibitors are routinely used for pharmacotherapy. However, most kinase inhibitors …