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
Identification of Small-Molecule Positive Modulators of Calcitonin-like Receptor-Based Receptors.
Erica R. Hendrikse,Lydia P. Liew,Rebekah L. Bower,Muriel Bonnet,Muhammad A. Jamaluddin,Nicole Prodan,Keith Richards,Christopher S. Walker,Garry Pairaudeau,David M. Smith,Roxana Maria Rujan,Risha Sudra,Christopher A. Reynolds,Jason M. Booe,Augen A. Pioszak,Jack U. Flanagan,Michael P. Hay,Debbie L. Hay +17 more
TL;DR: These are the first small-molecule positive modulators described for the CLR:RAMP complexes, and translational potential is shown as the compounds can positively modulate cAMP signaling in a vascular cell line model.
Journal ArticleDOI
Network Analysis Reveals the Recognition Mechanism for Dimer Formation of Bulb-type Lectins.
Yunjie Zhao,Yunjie Zhao,Yiren Jian,Zhichao Liu,Hang Liu,Qin Liu,Chanyou Chen,Zhangyong Li,Lu Wang,H. Howie Huang,Chen Zeng,Chen Zeng,Chen Zeng +12 more
TL;DR: A potential mechanism for this lectin complex formation where coevolving polar residues of high closeness are responsible for long-range recognition is proposed.
Journal ArticleDOI
Effect of mazEF, higBA and relBE toxin-antitoxin systems on antibiotic resistance in Pseudomonas aeruginosa and Staphylococcus isolates.
Umut Safiye Say Coskun,Ayşegül Çopur Çiçek,Cetin Kilinc,Rıdvan Güçkan,Yelda Dagcioglu,Osman Demir,Cemal Sandalli +6 more
TL;DR: The idea that resistance to antibiotics can be reduced by increasing TA gene expression levels is lead to the idea that it may be possible to have new sensitive regions in bacteria by activating TA systems.
Journal ArticleDOI
Deciphering the Preference and Predicting the Viability of Circular Permutations in Proteins
Wei-Cheng Lo,Wei-Cheng Lo,Tian Dai,Tian Dai,Yen Yi Liu,Li Fen Wang,Jenn-Kang Hwang,Ping-Chiang Lyu +7 more
TL;DR: The results fostered the development of an effective viable CP site prediction system, which combined four machine learning methods, e.g., artificial neural networks, the support vector machine, a random forest, and a hierarchical feature integration procedure developed in this work.
Journal ArticleDOI
Assortative mixing in close-packed spatial networks.
TL;DR: In this paper, a general analytical relation for the dependence of nearest neighbor degree correlations on degree is derived, which is shown to be the sole determining factor of assortative versus disassortative mixing in networks.
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.
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.
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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.
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.
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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.