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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Binding sites in protein structures: characterisation and relation with destabilising regions
TL;DR: A comprehensive approach to define binding sites unambiguously from structural data is undertaken, rigorously identified seven issues which should be considered when constructing datasets of binding sites to validate prediction methods, and the construction of two new datasets are presented.
Journal ArticleDOI
Full-scale network analysis reveals properties of the FV protein structure organization
A. J. Ferreira-Martins,Rodrigo Castaldoni,Brenno de Mello Alencar,Marcos Vinícius Ferreira,Tatiane De Araujo Nogueira,Ricardo Araújo Rios,Tiago J. S. Lopes +6 more
TL;DR: In this paper , a detailed network map of the Coagulation Factor V (FV) protein was created, where each node is a residue, and two residues are connected if they are in close proximity in the three-dimensional structure.
Journal ArticleDOI
Structural Insights into Phosphorylation-Mediated Polymerase Function Loss for DNA Polymerase β Bound to Gapped DNA
TL;DR: In this paper , the authors conducted atomistic molecular dynamics simulations of DNA polymerase β complexed with gapped DNA and revealed that phosphorylation at the S44 site, in the presence of Mg ions, induced significant conformational changes in the enzyme.
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.
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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.
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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.
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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.
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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.