Bioinformatics.: auth.: group Stasiak

 2018 May 2. doi: 10.1093/bioinformatics/bty365. [Epub ahead of print]

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



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.


Knoto-ID is written in C ++ and 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


PMID: 29722808