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
More filters
Posted ContentDOI
Topological Analysis of SARS CoV-2 Main Protease
TL;DR: There is an urgent necessity of effective medication against SARS CoV-2, which is producing the COVID-19 pandemic across the world, because its main protease (Mpro) represents an attractive pharmacological target due to its involvement in essential viral functions and the strongest inhibitors of this enzyme are those that produce the least change of this capacity of transmitting perturbations across the protein.
Journal ArticleDOI
Human Rhinovirus Inhibition Through Capsid “Canyon” Perturbation: Structural Insights into The Role of a Novel Benzothiophene Derivative
TL;DR: In this in silico report, residue interaction network analysis revealed that the binding of the benzothiophene derivative into the “canyon” region of the active site of HRV-B14 distorts its initially extensively networked and compact residue profile.
Journal ArticleDOI
Understanding large multiprotein complexes: applying a multiple allosteric networks model to explain the function of the Mediator transcription complex.
TL;DR: A model of network allostery and its application to the eukaryotic RNA polymerase II Mediator transcription complex suggests that protein complexes such as Mediator exist not only as physical but also as functional networks of interconnected proteins through which information is transferred from subunit to subunit by the propagation of an allosteric state known as conformational spread.
Journal ArticleDOI
The Inclusion of Water Molecules in Residue Interaction Networks Identifies Additional Central Residues.
TL;DR: It is found that the inclusion of water molecules in RINs leads to an increase in the number of central residues which adds a novel mechanism to the relevance of water molecule for protein function.
Book ChapterDOI
Understanding G Protein-Coupled Receptor Allostery via Molecular Dynamics Simulations: Implications for Drug Discovery.
TL;DR: A method for calculating the map of allosteric signal flow in different GPCR conformational states is described and how these concepts have been utilized in understanding the mechanism of GPCRs allostery are illustrated.
References
More filters
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.