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Nucleic Acids Research Advance Access published online on May 21, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm312
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Web Server Issue

Protein knot server: detection of knots in protein structures

Grigory Kolesov1, Peter Virnau2,3,*, Mehran Kardar2 and Leonid A. Mirny1,2,*

1Harvard–MIT Division of Health Sciences and Technology, 2Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA and 3Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg 7, 55099 Mainz, Germany

*To whom correspondence should be addressed. Tel: +1 617 452 4862; Fax: +1 617 253 2514; Email: leonid{at}mit.edu Corrrespondence may also be addressed to P. Virnau. Tel: 49 6131 3923646; Fax: 49 6131 3925441; Email: virnau{at}uni-mainz.de

Received January 31, 2007. Revised April 1, 2007. Accepted April 14, 2007.

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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