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Polymers 2017, 9(9), 444;

Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids

Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
Department of Mathematics, National Technical University of Athens, Zografou Campus, 15780 Athens, Greece
Vital-IT, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, IL 60607-7045, USA
Author to whom correspondence should be addressed.
Received: 26 August 2017 / Revised: 8 September 2017 / Accepted: 11 September 2017 / Published: 13 September 2017
(This article belongs to the Special Issue Knotted and Catenated Polymers)
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In this paper we introduce a method that offers a detailed overview of the entanglement of an open protein chain. Further, we present a purely topological model for classifying open protein chains by also taking into account any bridge involving the backbone. To this end, we implemented the concepts of planar knotoids and bonded knotoids. We show that the planar knotoids technique provides more refined information regarding the knottedness of a protein when compared to established methods in the literature. Moreover, we demonstrate that our topological model for bonded proteins is robust enough to distinguish all types of lassos in proteins. View Full-Text
Keywords: protein knots; knot theory; topology; knotoids protein knots; knot theory; topology; knotoids

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Goundaroulis, D.; Gügümcü, N.; Lambropoulou, S.; Dorier, J.; Stasiak, A.; Kauffman, L. Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids. Polymers 2017, 9, 444.

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