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Bioinformatics. 2018 Oct 1;34(19):3402-3404. doi: 10.1093/bioinformatics/bty365.

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

Author information

1
Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
2
Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
3
SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.

Abstract

Summary:

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.

Availability and implementation:

Knoto-ID is written in C++‚ÄČand includes R (www.R-project.org) scripts to generate plots of projections maps, fingerprint matrices and disk matrices. Knoto-ID is distributed under the GNU General Public License (GPL), version 2 or any later version and is available at https://github.com/sib-swiss/Knoto-ID. A binary distribution for Mac OS X, Linux and Windows with detailed user guide and examples can be obtained from https://www.vital-it.ch/software/Knoto-ID.

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