Journal ArticleDOI
Network analysis of protein structures identifies functional residues.
Gil Amitai,Arye Shemesh,Einat Sitbon,Maxim Shklar,Dvir Netanely,Ilya Venger,Shmuel Pietrokovski +6 more
TLDR
This work transformed protein structures into residue interaction graphs (RIGs), where amino acid residues are graph nodes and their interactions with each other are the graph edges, and found that active site, ligand-binding and evolutionary conserved residues, typically have high closeness values.About:
This article is published in Journal of Molecular Biology.The article was published on 2004-12-03. It has received 463 citations till now. The article focuses on the topics: Protein structure & Active site.read more
Citations
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Proceedings ArticleDOI
The scoring function based on amino acid network
Xiong Jiao,Lifeng Yang +1 more
TL;DR: It is found that the Sn scorning function has a better performance than the RP on some items and is proposed as a new docking scoring function Sn for 42 systems' bound docking results.
Proceedings ArticleDOI
JProNet: Systematic Network Analysis of Topological Properties of Protein 3D Structures
TL;DR: JProNet is a Java-based network tool for systematic analysis of structure-based topological properties of proteins that incorporates new developments in network theory such as the scale-free and the small-world properties.
Journal ArticleDOI
In Silico Study of Natural Xanthones as Potential Inhibitors of Alpha-Glucosidase and Alpha-Amylase
M. Jauhar,Isa Anshori,Michaella Yosephine,Putri Hawa Syaifie,Azza Hanif Harisna,Dwi Wahyu Nugroho,Etik Mardliyati,Adzani Gaisani Arda +7 more
TL;DR: This study performed molecular docking simulations on all 515 natural xanthones with alpha-glucosidase and alpha-amylase as the protein targets and revealed prenylated xanthone have a good potential as anti-type 2 diabetes mellitus agents through in silico method.
Proceedings ArticleDOI
Identifying the Nucleus Residues in Proteins by Network Approach
TL;DR: The protein structure is modeled as a network with the amino acid residues the vertices and contacts between them the edges and the nucleus residues of GB1 and CI2 are identified by the analysis of the network parameter: betweenness of transition states.
Journal ArticleDOI
Molecular characterization and computational structure prediction of activin receptor type IIB in aseel and broiler chicken
P. Guru Vishnu,T. K. Bhattacharya,Bharat Bhushan,Pushpendra Kumar,R.N. Chatterjee,C. Paswan,A. Rajendra Prasad,D. Divya,K. Dushyanth +8 more
TL;DR: The current research provides insights about structural and functional aspects of the receptor and also aids in understanding the evolutionary history of ACTRIIB.
References
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Journal ArticleDOI
Collective dynamics of small-world networks
TL;DR: Simple models of networks that can be tuned through this middle ground: regular networks ‘rewired’ to introduce increasing amounts of disorder are explored, finding that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs.
Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
Emergence of Scaling in Random Networks
TL;DR: A model based on these two ingredients reproduces the observed stationary scale-free distributions, which indicates that the development of large networks is governed by robust self-organizing phenomena that go beyond the particulars of the individual systems.
Journal ArticleDOI
Statistical mechanics of complex networks
TL;DR: In this paper, a simple model based on the power-law degree distribution of real networks was proposed, which was able to reproduce the power law degree distribution in real networks and to capture the evolution of networks, not just their static topology.
Journal ArticleDOI
Centrality in social networks conceptual clarification
TL;DR: In this article, three distinct intuitive notions of centrality are uncovered and existing measures are refined to embody these conceptions, and the implications of these measures for the experimental study of small groups are examined.