Abstract

KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several protein structures have been reported to contain intricate knots. The physiological role of knots and their effect on folding and evolution is an area of active research. The user submits a PDB id or uploads a 3D protein structure in PDB or mmCIF format. The current implementation of the server uses the Alexander polynomial to detect knots. The results of the analysis that are presented to the user are the location of the knot in the structure, the type of the knot and an interactive visualization of the knot. The results can also be downloaded and viewed offline. The server also maintains a regularly updated list of known knots in protein structures.

Keywords

UploadBiologyKnot (papermaking)Alexander polynomialProtein Data Bank (RCSB PDB)Web serverVisualizationComputer scienceKnot theoryThe InternetOperating systemArtificial intelligenceEngineering

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Publication Info

Year
2007
Type
article
Volume
35
Issue
Web Server
Pages
W425-W428
Citations
98
Access
Closed

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Cite This

Grigory Kolesov, Peter Virnau, Mehran Kardar et al. (2007). Protein knot server: detection of knots in protein structures. Nucleic Acids Research , 35 (Web Server) , W425-W428. https://doi.org/10.1093/nar/gkm312

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DOI
10.1093/nar/gkm312