Novel insights through the integration of structural and functional genomics data with protein networks
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TLDR
3D protein structures constitute a valuable conceptual and predictive framework by providing rational and compelling classification schemes for network elements, as well as revealing interesting intrinsic differences between distinct node types, such as disorder and evolutionary features, which may then be rationalized in light of their respective functions within networks.About:
This article is published in Journal of Structural Biology.The article was published on 2012-09-01 and is currently open access. It has received 20 citations till now. The article focuses on the topics: Systems biology.read more
Citations
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Journal ArticleDOI
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review
Peter Csermely,Tamas Korcsmaros,Tamas Korcsmaros,Huba Kiss,Gábor London,Ruth Nussinov,Ruth Nussinov +6 more
TL;DR: It is shown how network techniques can help in the identification of single-target, edgetic, multi-target and allo-network drug target candidates and an optimized protocol of network-aided drug development is suggested, and a list of systems-level hallmarks of drug quality is provided.
Book ChapterDOI
Intrinsically Disordered Proteins
TL;DR: This Sprenger Briefs volume is dedicated to IDPs and IDPRs and an attempt is made to compress a massive amount of knowledge and into a digest that aims to be of use to those wishing a fast entry into this promising field of structural biology.
Journal ArticleDOI
Genotype to phenotype via network analysis
TL;DR: How mutations may be treated as a perturbation of the molecular interaction network and what insights may be gained from taking this perspective are examined.
Journal ArticleDOI
The scoring of poses in protein-protein docking: current capabilities and future directions.
TL;DR: An evaluation of 115 scoring functions on an unbound docking decoy benchmark covering 118 complexes for which a near-native solution can be found, yielding top 10 success rates of up to 58%.
Journal ArticleDOI
RNase E in the γ-Proteobacteria: conservation of intrinsically disordered noncatalytic region and molecular evolution of microdomains.
TL;DR: A mechanism of microdomain acquisition and evolution is proposed and implications of these results for the structure and function of the multienzyme RNA degradosome are discussed.
References
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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.
Proceedings ArticleDOI
A training algorithm for optimal margin classifiers
TL;DR: A training algorithm that maximizes the margin between the training patterns and the decision boundary is presented, applicable to a wide variety of the classification functions, including Perceptrons, polynomials, and Radial Basis Functions.
Journal ArticleDOI
Error and attack tolerance of complex networks
TL;DR: It is found that scale-free networks, which include the World-Wide Web, the Internet, social networks and cells, display an unexpected degree of robustness, the ability of their nodes to communicate being unaffected even by unrealistically high failure rates.
Journal ArticleDOI
Sequencing technologies-the next generation
TL;DR: A technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments is presented.