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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

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



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 ( 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 A binary distribution for Mac OS X, Linux and Windows with detailed user guide and examples can be obtained from

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