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Nucleic Acids Research Advance Access originally published online on May 25, 2007
Nucleic Acids Research 2007 35(Web Server issue):W420-W424; doi:10.1093/nar/gkm304
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W420-W424
© 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.

Articles

pKNOT: the protein KNOT web server

Yan-Long Lai1, Shih-Chung Yen1, Sung-Huan Yu1 and Jenn-Kang Hwang1,2,*

1Institute of Bioinformatics, National Chiao Tung University, Hsinchu 30050, Taiwan and 2Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsinchu 30050, Taiwan

*To whom correspondence should be addressed. Tel: +886-3-513-1337; Fax: +886-3-572-9288; Email: jkhwang{at}cc.nctu.edu.tw

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

Knotted proteins are more commonly observed in recent years due to the enormously growing number of structures in the Protein Data Bank (PDB). Studies show that the knot regions contribute to both ligand binding and enzyme activity in proteins such as the chromophore-binding domain of phytochrome, ketol–acid reductoisomerase or SpoU methyltransferase. However, there are still many misidentified knots published in the literature due to the absence of a convenient web tool available to the general biologists. Here, we present the first web server to detect the knots in proteins as well as provide information on knotted proteins in PDB—the protein KNOT (pKNOT) web server. In pKNOT, users can either input PDB ID or upload protein coordinates in the PDB format. The pKNOT web server will detect the knots in the protein using the Taylor's smoothing algorithm. All the detected knots can be visually inspected using a Java-based 3D graphics viewer. We believe that the pKNOT web server will be useful to both biologists in general and structural biologists in particular.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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