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

Details

Serval ID
serval:BIB_6AEE0F404F13
Type
Article: article from journal or magazin.
Collection
Publications
Title
Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids.
Journal
Bioinformatics
Author(s)
Dorier J., Goundaroulis D., Benedetti F., Stasiak A.
ISSN
1367-4811 (Electronic)
ISSN-L
1367-4803
Publication state
Published
Issued date
01/10/2018
Peer-reviewed
Oui
Volume
34
Number
19
Pages
3402-3404
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
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.
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.
Keywords
Computational Biology, Protein Conformation, Proteins/chemistry, Software
Pubmed
Web of science
Create date
12/05/2018 11:06
Last modification date
26/10/2019 6:09
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