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
Computer-Based Screening of Functional Conformers of Proteins
TL;DR: A new method is described to discriminate protein conformations relevant to the specific recognition of a ligand based on a scoring system that matches critical residues with central residues in different structures of a given protein.
Journal ArticleDOI
webPDBinder: a server for the identification of ligand binding sites on protein structures
TL;DR: The webPDBinder correctly identifies residues belonging to the binding site in 77% of the cases and is able to identify binding pockets starting from holo or apo structures with comparable performances.
Journal ArticleDOI
On the structural context and identification of enzyme catalytic residues.
Yu-Tung Chien,Shao-Wei Huang +1 more
TL;DR: The structural context feature is combined with support vector machine to identify catalytic residues from enzyme structure and the prediction results are better or comparable to those of recent structure-based prediction methods.
Journal ArticleDOI
Computational characterization of the binding mode between oncoprotein Ets-1 and DNA-repair enzymes.
TL;DR: This study constitutes a first but important step in the characterization, at the molecular level, of the interaction between an oncoprotein and DNA‐repair enzymes, and rationalizes the binding mode using a series of computational analyses.
Journal ArticleDOI
Protein residue network analysis reveals fundamental properties of the human coagulation factor VIII.
Tiago J. S. Lopes,Ricardo Araújo Rios,Ricardo Araújo Rios,Tatiane C.A. Nogueira,Tatiane C.A. Nogueira,Rodrigo Fernandes de Mello,Rodrigo Fernandes de Mello +6 more
TL;DR: In this article, a residue interaction network (RIN) was proposed to identify important residues of coagulation factor VIII (FVIII) proteins and found important properties related to disease severity, interaction to other proteins and structural stability.
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.