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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Book ChapterDOI
Protein-Protein Interface and Disease: Perspective from Biomolecular Networks.
TL;DR: This review describes the different roles of protein complexes in disease through several structural aspects of interfaces and highlights possible future aspects of this area with respect to both methodology development and applications for disease treatment.
Journal ArticleDOI
Dynamics on human Toll-like receptor 4 complexation to MD-2: the coreceptor stabilizing function.
TL;DR: Both molecular dynamics and normal mode analysis reveled a stabilization of the terminal regions of hTLR4 upon complexation to MD‐2, and conserved important residues involved on the hTLr4–MD‐2 interaction dynamics are identified and disclosed.
Journal ArticleDOI
Network analysis of synonymous codon usage.
Khalique Newaz,Gabriel Wright,Jacob Piland,Jun Li,Patricia L. Clark,Scott J. Emrich,Tijana Milenkovic +6 more
TL;DR: In this paper, the authors use network centrality to measure the structural position of an amino acid and find that amino acids buried within the structural core are network-central, and those on the surface are not.
Book ChapterDOI
Analysis of Protein Structures Using Residue Interaction Networks
TL;DR: The applications of RIN are reviewed for the analysis and prediction of functionally important residues and ligand binding sites, protein–protein interactions, allosteric regulation, influence of point mutations on structure and dynamics of proteins.
Journal ArticleDOI
Network analysis of dynamically important residues in protein structures mediating ligand-binding conformational changes.
TL;DR: A network analysis of key positions of proteins reveals that the conformational diversity of proteins seems to be guaranteed by a network of strongly interconnected key positions rather than individual residues.
References
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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.