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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Journal ArticleDOI
Sequence Conservation, Radial Distance and Packing Density in Spherical Viral Capsids.
TL;DR: It is reported that, of the viral icosahedral capsids, the sequence conservation profile can be determined by variations in the distances between residues and the Centroid of the capsid – with a direct inverse proportionality between the conservation level and the centroid distance – as well as by the spatial variations in local packing density.
Posted ContentDOI
Bcl-xL dynamics and cancer-associated mutations under the lens of protein structure network and biomolecular simulations
Sora,Elena Papaleo +1 more
TL;DR: All-atom explicit solvent microsecond molecular dynamics simulations analyzed through a Protein Structure Network approach and integrated with calculations of changes in free energies upon cancer-related mutations identified by genomics studies found a subset of candidate residues responsible for both maintaining protein stability and for conveying structural information between the two binding sites.
Continuous-time quantum walks: simulation and application
TL;DR: This thesis introduces the classical and quantum walks, as well as key graph theory concepts that will underpin later results, and proposes a centrality measure based on the continuous-time quantum walk that is highly correlated with the classical eigenvector centrality and suggests that it provides an extension of the eigen vector centrality to the quantum realm.
Journal ArticleDOI
Comparing local search paths with global search paths on protein residue networks: allosteric communication
TL;DR: In this paper, the authors investigated the biological relevance of the differences in path characteristics on a type III receptor tyrosine kinase (KIT) and found that local search paths exhibit different characteristics from global search paths.
Proceedings ArticleDOI
NetGist: Learning to Generate Task-Based Network Summaries
TL;DR: This paper proposes NetGist, a framework which automatically learns how to generate a summary for a given task on a given network, and robustly and effectively learns meaningful summaries, and helps solve challenging problems, and aids in complex task-based sense-making of networks.
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.