PyKnot: a PyMOL tool for the discovery and analysis of knots in proteins

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.