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arXiv · 1806.01675

Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids

Julien Dorier·Dimos Goundaroulis·Fabrizio Benedetti·Andrzej Stasiak
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Abstract

The backbone of most proteins forms an open curve. To study their entanglement, a common strategy consists in searching for the presence of knots in their backbones using topological invariants. However, this approach requires to close the curve into a loop, which alters the geometry of curve. Knoto-ID allows evaluating the entanglement of open curves without the need to close them, using the recent concept of knotoids which is a generalization of the classical knot theory to open curves. Knoto-ID can analyse the global topology of the full chain as well as the local topology by exhaustively studying all subchains or only determining the knotted core. Knoto-ID permits to localize topologically non-trivial protein folds that are not detected by informatics tools detecting knotted protein folds.

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Julien Dorier, Dimos Goundaroulis, Fabrizio Benedetti, Andrzej Stasiak. 2018-06-05. Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids. https://doi.org/10.1093/bioinformatics%2Fbty365

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