Protein Network Analysis of the Fifth Chromosome of Zebrafish

2020 ◽  
Vol 27 (5) ◽  
pp. 729-737
Author(s):  
Lei Li ◽  
Linhua Jiang ◽  
Sihua Peng
Keyword(s):  
Network Analysis ◽  
Protein Network

scholarly journals Combinatorial RNAi for quantitative protein network analysis

2007 ◽  
Vol 104 (16) ◽  
pp. 6579-6584 ◽  
Author(s):  
O. Sahin ◽  
C. Lobke ◽  
U. Korf ◽  
H. Appelhans ◽  
H. Sultmann ◽  
...  
Keyword(s):  
Network Analysis ◽  
Protein Network

scholarly journals Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis

2011 ◽  
Vol 40 (D1) ◽  
pp. D465-D471 ◽  
Author(s):  
J. Lees ◽  
C. Yeats ◽  
J. Perkins ◽  
I. Sillitoe ◽  
R. Rentzsch ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Network Analysis ◽  
Functional Annotation ◽  
Protein Network

scholarly journals Mapping Novel Copper-Regulated Signalling Pathways Using Antibody Arrays and in Silico Protein Network Analysis

2008 ◽  
Vol S2 (01) ◽  
pp. 056-057
Author(s):  
A. R. White ◽  
T. Du ◽  
L. Bica ◽  
A. Caragounis ◽  
K. A. Price ◽  
...  
Keyword(s):  
Network Analysis ◽  
In Silico ◽  
Protein Network ◽  
Signalling Pathways ◽  
Antibody Arrays

scholarly journals A Connectivity Map-Based Drug Repurposing Study and Integrative Analysis of Transcriptomic Profiling of SARS-CoV-2 Infection

2020 ◽  
Author(s):  
seyedeh zahra mousavi ◽  
mojdeh rahmanian ◽  
ashkan sami
Keyword(s):  
Network Analysis ◽  
Cell Line ◽  
Inhaled Corticosteroids ◽  
Drug Repurposing ◽  
Protein Network ◽  
New Drugs ◽  
Health Concern ◽  
Epithelial Cell Line ◽  
Connectivity Map ◽  
Pathway Enrichment

<div>Aims: The recent outbreak of COVID-19 has become a global health concern. There are currently no effective treatment strategies and vaccines for the treatment or prevention of this fatal disease. The current study aims to determine promising treatment options for the COVID-19 through a computational drug repurposing approach.</div><div>Materials and methods: In this study, we focus on differentially expressed genes (DEGs), detected in SARS-CoV-2 infected cell lines including “the primary human lung epithelial cell line NHBE” and “the transformed lung alveolar cell line A549”. Next, the identified DEGs are used in the connectivity map (CMap) analysis to identify similarly acting therapeutic candidates. Furthermore, to interpret lists of DEGs, pathway enrichment and protein network analysis are performed. Genes are categorized into easily interpretable pathways based on their biological functions, and overrepresentations of each pathway are tested in comparison to what is expected randomly.</div><div>Key findings: The results suggest the effectiveness of Saquinavir, lansoprazole, folic acid, ebselen, aminocaproic acid, simvastatin, surfactant stimulant drugs, heat shock protein 90 (HSP90) inhibitors, histone deacetylase (HDAC) inhibitors, metronidazole, inhaled corticosteroids (ICS) and many other clinically approved drugs and investigational compounds as potent drugs against COVID-19 outbreak.</div><div>Significance: Making new drugs remain a lengthy process, so the drug repurposing approach provides an insight into the therapeutics that might be helpful in this pandemic. In this study, pathway enrichment and protein network analysis are also performed, and the effectiveness of some drugs obtained from the CMap analysis has been investigated according to previous research.</div>

Rational engineering of ornithine decarboxylase with greater selectivity for ornithine over lysine through protein network analysis

2018 ◽  
Vol 281 ◽  
pp. 175-182 ◽  
Author(s):  
Eun Young Hong ◽  
Jin Young Kim ◽  
Roopali Upadhyay ◽  
Byung Jun Park ◽  
Jong Min Lee ◽  
...  
Keyword(s):  
Network Analysis ◽  
Ornithine Decarboxylase ◽  
Protein Network ◽  
Rational Engineering

scholarly journals Theoretical Study on Zearalenol Compounds Binding with Wild Type Zearalenone Hydrolase and V153H Mutant

2018 ◽  
Vol 19 (9) ◽  
pp. 2808 ◽  
Author(s):  
Ye Liu ◽  
Youzhong Wan ◽  
Jingxuan Zhu ◽  
Zhengfei Yu ◽  
Xiaopian Tian ◽  
...  
Keyword(s):  
Network Analysis ◽  
Specific Activity ◽  
Protein Network ◽  
Side Chain ◽  
Cereal Crops ◽  
Wild Type ◽  
High Betweenness ◽  
Theoretical Evidence ◽  
Dynamics Simulations ◽  
Theoretical Results

Zearalenone hydrolase (ZHD) is the only reported α/β-hydrolase that can detoxify zearalenone (ZEN). ZHD has demonstrated its potential as a treatment for ZEN contamination that will not result in damage to cereal crops. Recent researches have shown that the V153H mutant ZHD increased the specific activity against α-ZOL, but decreased its specific activity to β-ZOL. To understand whyV153H mutation showed catalytic specificity for α-ZOL, four molecular dynamics simulations combining with protein network analysis for wild type ZHD α-ZOL, ZHD β-ZOL, V153H α-ZOL, and V153H β-ZOL complexes were performed using Gromacs software. Our theoretical results indicated that the V153H mutant could cause a conformational switch at the cap domain (residues Gly161–Thr190) to affect the relative position catalytic residue (H242). Protein network analysis illustrated that the V153H mutation enhanced the communication with the whole protein and residues with high betweenness in the four complexes, which were primarily assembled in the cap domain and residues Met241 to Tyr245 regions. In addition, the existence of α-ZOL binding to V153H mutation enlarged the distance from the OAE atom in α-ZOL to the NE2 atom in His242, which prompted the side chain of H242 to the position with catalytic activity, thereby increasing the activity of V153H on the α-ZOL. Furthermore, α-ZOL could easily form a right attack angle and attack distance in the ZHD and α-ZOL complex to guarantee catalytic reaction. The alanine scanning results indicated that modifications of the residues in the cap domain produced significant changes in the binding affinity for α-ZOL and β-ZOL. Our results may provide useful theoretical evidence for the mechanism underlying the catalytic specificity of ZHD.

scholarly journals DiSWOP: a novel measure for cell-level protein network analysis in localized proteomics image data

2013 ◽  
Vol 30 (3) ◽  
pp. 420-427 ◽  
Author(s):  
Violeta N. Kovacheva ◽  
Adnan M. Khan ◽  
Michael Khan ◽  
David B. A. Epstein ◽  
Nasir M. Rajpoot
Keyword(s):  
Network Analysis ◽  
Image Data ◽  
Protein Network ◽  
Cell Level
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