Protein knot server: detection of knots in protein structures

被引：80

作者：

Kolesov, Grigory ^{[1
]}

Virnau, Peter ^{[2
,3
]}

Kardar, Mehran ^{[2
]}

Mirny, Leonid A. ^{[1
,2
]}

机构：

[1] MIT, Dept Phys, Cambridge, MA 02139 USA

[2] Harvard Univ, MIT, Div Hlth Sci & Technol, Cambridge, MA 02139 USA

[3] Johannes Gutenberg Univ Mainz, Inst Phys, D-55099 Mainz, Germany

来源：

NUCLEIC ACIDS RESEARCH | 2007年 / 35卷

基金：

美国国家科学基金会;

关键词：

D O I：

10.1093/nar/gkm312

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：W425 / W428

页数：4

共 25 条

[1]

Adams C., 1994, The Knot Book: An Elementary Introduction to the Mathematical Theory of Knots

[2] Knotting probability of DNA molecules confined in restricted volumes:: DNA knotting in phage capsids [J].