A similarity network approach for the analysis and comparison of protein sequence/structure sets

Journal of Biomedical Informatics
Ioannis ValavanisKonstantina Nikita

Abstract

A set of proteins is a complex system whose elements are interrelated on the concept of sequence- and structure-based similarity. Here, we applied a similarity network-based methodology for the representation and analysis of protein sequences and structures sets using a non-redundant set of 311 proteins and three different information criteria based on sequence-derived features, sequence local alignment and structural alignment. A wide set of measurements, like network degree, clustering coefficient, characteristic path length and vertex centrality were utilized to characterize the networks' topology. Protein similarity networks were found medium or highly interconnected and the existence of both clusters and random edges classified their fully connected versions as Small World Networks (SWNs). The SWN architecture was able to host the continuous similarity transition among proteins and model the protein information flow during evolution. Recently reported ancestral elements, like the alpha/beta class and certain folds, were remarkably found to act as hubs in the networks. Additionally, the moderate information value of sequence-derived features when used for fold and class assignment was shown on a network basis. The methodolo...Continue Reading

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Citations

Nov 23, 2013·PloS One·Alberto J M MartinSilvio C E Tosatto
Sep 22, 2015·Frontiers in Pharmacology·Tiago J S LopesHiroaki Kitano
Aug 26, 2014·Journal of Bioinformatics and Computational Biology·Christos LamprosDimitrios I Fotiadis
Oct 23, 2015·Journal of the Royal Society, Interface·Vladimir Gligorijević, Nataša Pržulj
Mar 3, 2012·PLoS Computational Biology·Vered KunikYanay Ofran
Apr 4, 2017·Database : the Journal of Biological Databases and Curation·Gemma L HollidayPatricia C Babbitt
May 7, 2019·Journal of Bioinformatics and Computational Biology·Farzad PeyraviSeyed Mohammad Moshtaghioun
Dec 12, 2018·Bulletin of Mathematical Biology·Farzad PeyraviSeyed Mohammad Moshtaghioun
Apr 25, 2020·Journal of Molecular Biology·Noelia FerruzBirte Höcker
Dec 14, 2018··Hamza HanafiBadr Dine Rossi Hassani

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