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Updated: Jul 14, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Protein knot server: detection of knots in protein structures
Grigory Kolesov1, Peter Virnau, Mehran Kardar
1Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA.
Nucleic Acids Research
|May 23, 2007
Summary
The KNOTS web server identifies complex knots in protein structures using the Alexander polynomial. This tool aids research into the function and evolution of these intricate protein formations.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Protein structures can exhibit complex knot topologies.
- The biological significance of protein knots in folding and evolution is under investigation.
Purpose of the Study:
- To introduce KNOTS, a web server for detecting knots in protein 3D structures.
- To provide researchers with a tool for analyzing and visualizing protein knot topology.
Main Methods:
- Utilizes the Alexander polynomial for knot detection.
- Accepts Protein Data Bank (PDB) or mmCIF format for structure input.
- Provides interactive 3D visualization of detected knots.
Main Results:
- Identifies the location and type of knots within protein structures.
- Offers downloadable results for offline analysis.
- Maintains an updated database of known protein knots.
Conclusions:
- KNOTS serves as a valuable resource for studying protein knot structures.
- Facilitates research on the roles of knots in protein folding, function, and evolution.
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The primary structure of a protein is its amino acid sequence.
The primary structure of a protein is its amino acid sequence.
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Overview