scholarly journals Time Series Analysis on the Conformational Change of c-Src Tyrosine Kinase

2021 ◽  
Author(s):  
Hyun Jung Yoon ◽  
Sungmin Lee ◽  
Suhyun Park ◽  
Sangwook Wu
Keyword(s):  
Time Series ◽  
Tyrosine Kinase ◽  
Conformational Change ◽  
Active Form ◽  
Closeness Centrality ◽  
Dynamics Simulation ◽  
Centrality Measures ◽  
Signal Transduction Pathways ◽  
Degree Centrality ◽  
Src Tyrosine Kinase

c-Src tyrosine kinase plays an important role in signal transduction pathways, where its activity is regulated by phosphorylation of the two tyrosine residues. We performed targeted molecular dynamics simulation to obtain trajectory of conformational change from inactive to active form. To investigate the conformational change of c-Src tyrosine kinase, we applied network analysis to time series of correlation among residues. The time series of correlation between residues during the conformational change generated by targeted molecular dynamic simulation. With centrality measures such as betweenness centrality, degree centrality, and closeness centrality, we observed a few important residues that significantly contribute to the conformational change of c-Src tyrosine kinase for the different time steps.

scholarly journals A COMPARISON OF CENTRALITY MEASURES IN SUSTAINABLE DEVELOPMENT GOALS

2020 ◽  
Vol 14 (3) ◽  
pp. 309-320
Author(s):  
Sena Ariesandy ◽  
Ema Carnia ◽  
Herlina Napitupulu
Keyword(s):  
Sustainable Development ◽  
Millennium Development Goals ◽  
Sustainable Development Goals ◽  
Closeness Centrality ◽  
Centrality Measures ◽  
Degree Centrality ◽  
Eigenvector Centrality ◽  
Global Problems ◽  
Calculation Results ◽  
Development Goals

The Millennium Development Goals (MDGs), which began in 2000 with 8 goal points, have not been able to solve the global problems. The MDGs were developed into Sustainable Development Goals (SDGs) in 2015 with 17 targeted goal points achieved in 2030. Until now, methods for determining the priority of SDGs are still attractive to researchers. Centrality is one of the tools in determining the priority goal points on a network by using graph theory. There are four measurements of centrality used in this paper, namely degree centrality, betweenness centrality, closeness centrality, and eigenvector centrality. The calculation results obtained from the four measurements are compared, analyzed, to conclud which goal points are the most prior and the least prior. From the results obtained the most priority goal points in Sustainable Development Goals.

Temporal Variation of the Node Centrality Metrics for Scale-Free Networks

2018 ◽  
pp. 78-97
Keyword(s):  
Temporal Variation ◽  
Closeness Centrality ◽  
The Other ◽  
Centrality Measures ◽  
Degree Centrality ◽  
Eigenvector Centrality ◽  
Scale Free ◽  
Centrality Metrics ◽  
Scale Free Networks ◽  
Free Network

Scale-free networks are a type of complex networks in which the degree distribution of the nodes is according to the power law. In this chapter, the author uses the widely studied Barabasi-Albert (BA) model to simulate the evolution of scale-free networks and study the temporal variation of degree centrality, eigenvector centrality, closeness centrality, and betweenness centrality of the nodes during the evolution of a scale-free network according to the BA model. The model works by adding new nodes to the network, one at a time, with the new node connected to m of the currently existing nodes. Accordingly, nodes that have been in the network for a longer time have greater chances of acquiring more links and hence a larger degree centrality. While the degree centrality of the nodes has been observed to show a concave down pattern of increase with time, the temporal (time) variation of the other centrality measures has not been analyzed until now.

scholarly journals A New Monoclonal Antibody Which Selectively Recognizes the Active Form of Src Tyrosine Kinase

1996 ◽  
Vol 271 (10) ◽  
pp. 5680-5685 ◽  
Author(s):  
Hisaaki Kawakatsu ◽  
Takao Sakai ◽  
Yumiko Takagaki ◽  
Yasuhiko Shinoda ◽  
Masaki Saito ◽  
...  
Keyword(s):  
Monoclonal Antibody ◽  
Tyrosine Kinase ◽  
Active Form ◽  
Src Tyrosine Kinase

A Study on Imatinib Binding to c-Src Tyrosine Kinase According to Sequential Conformational Change

2019 ◽  
Vol 69 (9) ◽  
pp. 984-988
Author(s):  
Suhyun PARK ◽  
Sangwook WU*
Keyword(s):  
Tyrosine Kinase ◽  
Conformational Change ◽  
Src Tyrosine Kinase

scholarly journals A Survey on Recent Methods of Finding Influential Nodes in Complex Networks

2021 ◽  
Vol 10 (2) ◽  
pp. 816-823
Keyword(s):  
Complex Networks ◽  
Time Complexity ◽  
Closeness Centrality ◽  
Clustering Coefficient ◽  
Centrality Measures ◽  
Degree Centrality ◽  
Computation Complexity ◽  
Influential Nodes ◽  
New Challenges ◽  
Virus Spreading

Influential nodes refer to the ability of a node to spread information in complex networks. Identifying influential nodes is an important problem in complex networks which plays a key role in many applications such as rumor controlling, virus spreading, viral market advertising, research paper views, and citations. Basic measures like degree centrality, betweenness centrality, closeness centrality are identifying influential nodes but they are incapable of largescale networks due to time complexity issues. Chen et al. [1] proposed semi-local centrality, which is reducing computation complexity and finding influential nodes in the network. Recently Yang et al. 2020 [2] proposed a novel centrality measure based on degree and clustering coefficient for identifying the influential nodes. Sanjay et al. 2020 [3] gave voterank and neighborhood coreness-based algorithms for finding the influenced nodes in the network. Zhiwei et al. 2019 [4] considered the average shortest path to discover the influenced node in the network. These are the few recent local,global and mixed centralities. In this paper, we show a broad view of recent methods for finding influential nodes in complex networks. It also analyzes the new challenges and limitations for a better understanding of each method in detail. The experimental results based on these methods show better performance compared with existing basic centrality measures.

scholarly journals Network approach of the conformational change of c-Src, a tyrosine kinase, by molecular dynamics simulation

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Hyun Jung Yoon ◽  
Sungmin Lee ◽  
Sun Joo Park ◽  
Sangwook Wu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Tyrosine Kinase ◽  
Conformational Change ◽  
Dynamics Simulation ◽  
Network Approach
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