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A Topological Framework for the Computation of the HOMFLY Polynomial and Its Application to Proteins

Polymers can be modeled as open polygonal paths and their closure generates knots. Knotted proteins detection is currently achieved via high-throughput methods based on a common framework insensitive to the handedness of knots. Here we propose a topological framework for the computation of the HOMFL...

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Detalles Bibliográficos
Autores principales: Comoglio, Federico, Rinaldi, Maurizio
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3076383/
https://www.ncbi.nlm.nih.gov/pubmed/21533239
http://dx.doi.org/10.1371/journal.pone.0018693
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author Comoglio, Federico
Rinaldi, Maurizio
author_facet Comoglio, Federico
Rinaldi, Maurizio
author_sort Comoglio, Federico
collection PubMed
description Polymers can be modeled as open polygonal paths and their closure generates knots. Knotted proteins detection is currently achieved via high-throughput methods based on a common framework insensitive to the handedness of knots. Here we propose a topological framework for the computation of the HOMFLY polynomial, an handedness-sensitive invariant. Our approach couples a multi-component reduction scheme with the polynomial computation. After validation on tabulated knots and links the framework was applied to the entire Protein Data Bank along with a set of selected topological checks that allowed to discard artificially entangled structures. This led to an up-to-date table of knotted proteins that also includes two newly detected right-handed trefoil knots in recently deposited protein structures. The application range of our framework is not limited to proteins and it can be extended to the topological analysis of biological and synthetic polymers and more generally to arbitrary polygonal paths.
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spelling pubmed-30763832011-04-29 A Topological Framework for the Computation of the HOMFLY Polynomial and Its Application to Proteins Comoglio, Federico Rinaldi, Maurizio PLoS One Research Article Polymers can be modeled as open polygonal paths and their closure generates knots. Knotted proteins detection is currently achieved via high-throughput methods based on a common framework insensitive to the handedness of knots. Here we propose a topological framework for the computation of the HOMFLY polynomial, an handedness-sensitive invariant. Our approach couples a multi-component reduction scheme with the polynomial computation. After validation on tabulated knots and links the framework was applied to the entire Protein Data Bank along with a set of selected topological checks that allowed to discard artificially entangled structures. This led to an up-to-date table of knotted proteins that also includes two newly detected right-handed trefoil knots in recently deposited protein structures. The application range of our framework is not limited to proteins and it can be extended to the topological analysis of biological and synthetic polymers and more generally to arbitrary polygonal paths. Public Library of Science 2011-04-13 /pmc/articles/PMC3076383/ /pubmed/21533239 http://dx.doi.org/10.1371/journal.pone.0018693 Text en Comoglio, Rinaldi. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Comoglio, Federico
Rinaldi, Maurizio
A Topological Framework for the Computation of the HOMFLY Polynomial and Its Application to Proteins
title A Topological Framework for the Computation of the HOMFLY Polynomial and Its Application to Proteins
title_full A Topological Framework for the Computation of the HOMFLY Polynomial and Its Application to Proteins
title_fullStr A Topological Framework for the Computation of the HOMFLY Polynomial and Its Application to Proteins
title_full_unstemmed A Topological Framework for the Computation of the HOMFLY Polynomial and Its Application to Proteins
title_short A Topological Framework for the Computation of the HOMFLY Polynomial and Its Application to Proteins
title_sort topological framework for the computation of the homfly polynomial and its application to proteins
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3076383/
https://www.ncbi.nlm.nih.gov/pubmed/21533239
http://dx.doi.org/10.1371/journal.pone.0018693
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