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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Autores principales:	Federico Comoglio, Maurizio Rinaldi
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/93fb7e63974240bba5b0d453068107ee
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id	oai:doaj.org-article:93fb7e63974240bba5b0d453068107ee
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spelling	oai:doaj.org-article:93fb7e63974240bba5b0d453068107ee2021-11-18T06:55:49ZA topological framework for the computation of the HOMFLY polynomial and its application to proteins.1932-620310.1371/journal.pone.0018693https://doaj.org/article/93fb7e63974240bba5b0d453068107ee2011-04-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21533239/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Polymers 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.Federico ComoglioMaurizio RinaldiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 4, p e18693 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Federico Comoglio Maurizio Rinaldi A topological framework for the computation of the HOMFLY polynomial and its application to proteins.
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.
format	article
author	Federico Comoglio Maurizio Rinaldi
author_facet	Federico Comoglio Maurizio Rinaldi
author_sort	Federico Comoglio
title	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_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_sort	topological framework for the computation of the homfly polynomial and its application to proteins.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/93fb7e63974240bba5b0d453068107ee
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A topological framework for the computation of the HOMFLY polynomial and its application to proteins.

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