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

Détails

ID Serval
serval:BIB_6AEE0F404F13
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids.
Périodique
Bioinformatics
Auteur(s)
Dorier J., Goundaroulis D., Benedetti F., Stasiak A.
ISSN
1367-4811 (Electronic)
ISSN-L
1367-4803
Statut éditorial
Publié
Date de publication
01/10/2018
Peer-reviewed
Oui
Volume
34
Numéro
19
Pages
3402-3404
Langue
anglais
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Résumé
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 (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.
Mots-clé
Computational Biology, Protein Conformation, Proteins/chemistry, Software
Pubmed
Web of science
Création de la notice
12/05/2018 10:06
Dernière modification de la notice
26/10/2019 5:09
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