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
Journal ArticleDOI
Discovery of Functional Motifs from the Interface Region of Oligomeric Proteins Using Frequent Subgraph Mining
TL;DR: In this paper, a scalable algorithm for frequent subgraph mining was proposed for the discovery of functional motifs that exist along the interface region of a given protein complex, based on graph mining.
Journal Article
Network analysis of transcription factors for nuclear reprogramming into induced pluripotent stem cell using bioinformatics.
TL;DR: This study has shown an innovative rapid method for the analysis of intra and inter-networking among nuclear reprogramming factors and may aid researchers to understand the complex regulatory networks involving iPS cell generation.
Journal ArticleDOI
Phosphorylation Induced Conformational Transitions in DNA Polymerase β
TL;DR: A comprehensive atomic resolution study of wild type and phosphorylated DNA polymerase using molecular dynamics simulations and reveals that the S44 phosphorylation causes structural rearrangements and modulates the information pathway between the Lyase domain and base pair binding domain.
Dissertation
Statistical and Relational Learning for Understanding Enzyme Function
TL;DR: This thesis proposes novel statistical relational approaches for mining hierarchical features for multiple related tasks and a relational approach is proposed for exploiting the learnt relational rules for generating novel mutations with specific characteristics.
Journal ArticleDOI
Graphs of Hydrogen-Bond Networks to Dissect Protein Conformational Dynamics.
TL;DR: Applications of graph-based algorithms to dissect dynamical hydrogen-bond networks of protein complexes, with illustrations for GPCRs and spike protein S, are discussed.
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.