• KnotFind

The code accepts a .pdb file as a input parameter and searches the entire chain of Alpha Carbons for knots by trimming residues one at a time and ends up with either no knots or the smallest knot core that is found.

• SlipKnot Detector

A slipknot is formed when the remainder of the knotted protien double backs on itself, making the traditional knotfind algorithms not detect it as a knot. This algorithm here searches for the k1 atom with which the knot can be removed by a simple pull. If the protein has a slipknot, it returns a .pdb file with core of the slipknot.

• Python: PyMol Visualization

A simple python script using the PyMol API to connect all the Alpha Carbons using the cmd.bond() method and then coloring it using cmd.spectrum().