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PyLink: a PyMOL plugin to identify links

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dc.abstract.enSummary: Links are generalization of knots, that consist of several components. They appear in proteins, peptides and other biopolymers with disulfide bonds or ions interactions giving rise to the exceptional stability. Moreover because of this stability such biopolymers are the target of commercial and medical use (including anti-bacterial and insecticidal activity). Therefore, topological characterization of such biopolymers, not only provides explanation of their thermodynamical or mechanical properties, but paves the way to design templates in pharmaceutical applications. However, distinction between links and trivial topology is not an easy task. Here, we present PyLink – a PyMOL plugin suited to identify three types of links and perform comprehensive topological analysis of proteins rich in disulfide or ion bonds. PyLink can scan for the links automatically, or the user may specify their own components, including closed loops with several bridges and ion interactions. This creates the possibility of designing new biopolymers with desired properties. Availability and implementation: The PyLink plugin, manual, and tutorial videos are available at http://pylink.cent.uw.edu.pl Contact: jsulkowska@chem.uw.edu.pl
dc.affiliationUniwersytet Warszawski
dc.contributor.authorNiemyska, Wanda
dc.contributor.authorGierut, Aleksandra
dc.contributor.authorDąbrowski-Tumański, Paweł
dc.contributor.authorMillett, Kenneth
dc.contributor.authorSułkowska, Joanna
dc.date.accessioned2024-01-25T18:42:49Z
dc.date.available2024-01-25T18:42:49Z
dc.date.issued2019
dc.description.financeNie dotyczy
dc.description.number17
dc.description.volume35
dc.identifier.doi10.1093/BIOINFORMATICS/BTY1038
dc.identifier.issn1367-4803
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/117627
dc.languageeng
dc.relation.ispartofBioinformatics
dc.relation.pages3166–3168
dc.rightsClosedAccess
dc.sciencecloudnosend
dc.titlePyLink: a PyMOL plugin to identify links
dc.typeJournalArticle
dspace.entity.typePublication