Biology – Quantitative Biology – Biomolecules
Scientific paper
2011-04-18
PLoS ONE 6(4): e18693 (2011)
Biology
Quantitative Biology
Biomolecules
20 pages, 7 figures
Scientific paper
10.1371/journal.pone.0018693
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.
Comoglio Federico
Rinaldi Maurizio
No associations
LandOfFree
A Topological Framework for the Computation of the HOMFLY Polynomial and Its Application to Proteins does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with A Topological Framework for the Computation of the HOMFLY Polynomial and Its Application to Proteins, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and A Topological Framework for the Computation of the HOMFLY Polynomial and Its Application to Proteins will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-71587