a topological framework for the computation of the homfly polynomial and its application to proteins拓扑框架homfly多项式的计算及其应用蛋白质.pdfVIP

A Topological Framework for the Computation of the HOMFLY Polynomial and Its Application to Proteins ¤ Federico Comoglio , Maurizio Rinaldi* Department of Chemical, Food, Pharmaceutical and Pharmacological Sciences (DiSCAFF), University of Piemonte Orientale ‘‘Amedeo Avogadro’’, Novara, Italy 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. Citation: Comoglio F, Rinaldi M (2011) A Topological Framework for the Computation of the HOMFLY Polynomial and Its Application to Proteins. PLoS ONE 6(4): e18693. doi:10.1371/journal.pone.0018693 Editor: Darren R Flower, Aston University, United Kingdom Received December 16, 2010; Accepted March 8, 2011; Published April 13, 2011 Copyright: 2011 Comoglio, Rinaldi. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits