Protein knot server: detection of knots in protein structures

• Main Authors: Kolesov, Grigory (Contributor), Virnau, Peter (Contributor), Kardar, Mehran (Contributor), Mirny, Leonid A. (Contributor)
• Other Authors: Whitaker College of Health Sciences and Technology (Contributor), Harvard University- (Contributor), Massachusetts Institute of Technology. Department of Physics (Contributor)
• Format: Article
• Language: English
• Published: Oxford University Press, 2012-08-22T20:06:05Z.
• Subjects: Article
• Online Access: Get fulltext

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.
National Science Foundation (U.S.) (grant DMR-04-26677)
Deutsche Forschungsgemeinschaft (DFG) (grant VI237/1)
Alfred P. Sloan Foundation (Research Fellowship)