ArticlePloS one2011
A topological framework for the computation of the HOMFLY polynomial and its application to proteins.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Simulations of knotting of DNA during genome mapping.Biomicrofluidics · 2017Article
- KnotProt: a database of proteins with knots and slipknots.Nucleic acids research · 2015Article
- A general method for computing the Homfly polynomial of DNA double crossover 3-regular links.PloS one · 2015Article
- Knot theory in understanding proteins.Journal of mathematical biology · 2012Review
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2 authors.
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Abstract
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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