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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The effect of edge definition of complex networks on protein structure identification.
TL;DR: The identification performance of 2847 proteins with domain/domains proved that the structure of proteins was described well, and the optimal cutoff value for constructing the protein structure networks was 5.0 Å while the ideal community division method was community structure detection based on edge betweenness in this study.
Journal ArticleDOI
Bcl-xL Dynamics under the Lens of Protein Structure Networks.
TL;DR: In this paper, the authors investigated the distal communication between these two sites in B-cell lymphoma extra-large (Bcl-xL) in its free state and when bound to PUMA and found a subset of candidate residues responsible for both maintaining protein stability and for conveying structural information between the two binding sites.
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Automatic prediction of flexible regions improves the accuracy of protein-protein docking models.
TL;DR: A general method to automatically identify the flexible hinges for domain assembly and the flexible loops for loop refinement, in addition to predicting the corresponding movements of the identified active residues, is proposed.
Journal ArticleDOI
Molecular dynamics simulations provide structural insight into binding of cyclic dinucleotides to human STING protein.
TL;DR: Sarma et al. as discussed by the authors used molecular dynamics simulations to investigate dynamical aspects of binding of cyclic dinucleotides (CDNs) with human stimulator of interferon genes (hSTING).
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RiSLnet: Rapid identification of smart mutant libraries using protein structure network. Application to thermal stability enhancement.
TL;DR: A method called RiSLnet (Rapid identification of Smart mutant Library using residue network) to identify specific target residues by combining network analysis for protein residue interactions, identification of conserved residues, and evaluation of relative solvent accessibility is proposed.
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.
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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.