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Updated: May 22, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
PyKnot: a PyMOL tool for the discovery and analysis of knots in proteins
1Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. rhonald.lua@gmail.com
Summary:
Understanding the differences between knotted and unknotted protein structures may offer insights into how proteins fold. To characterize the type of knot in a protein, we have developed PyKnot, a plugin that works seamlessly within the PyMOL molecular viewer and gives quick results including the knot's invariants, crossing numbers and simplified knot projections and backbones. PyKnot may be useful to researchers interested in classifying knots in macromolecules and provides tools for students of biology and chemistry with which to learn topology and macromolecular visualization.
Availability:
PyMOL is available at http://www.pymol.org. The PyKnot module and tutorial videos are available at http://youtu.be/p95aif6xqcM.
Contact:
rhonald.lua@gmail.com.
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