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. 2007 Jul;35(Web Server issue):W425-8.
doi: 10.1093/nar/gkm312. Epub 2007 May 21.

Protein knot server: detection of knots in protein structures

Grigory Kolesov  1 , Peter Virnau, Mehran Kardar, Leonid A Mirny
Affiliations

Protein knot server: detection of knots in protein structures

Grigory Kolesov et al. Nucleic Acids Res. 2007 Jul.

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.

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Figures

Figure 1.
Figure 1.
The output of the Knots server for H. influenzae TrmD (PDB id 1uam). (A) Page one: the summary table. (B) Page two: Jmol interactive visualization. The 1uam structure is displayed in the left window with a knot highlighted in rainbow colors and the rest of the protein hidden. In this case, the trefoil knot spans a relatively small region of the protein and can be easily seen by eye in the protein structure. In many cases, this is difficult and the right panel offers the view of a simplified (reduced) representation of the knot. These visualizations can also be viewed offline using Rasmol scripts provided in the downloadable package.
See this image and copyright information in PMC

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