iPython notebook and supporting data to accompany "The SKMT Algorithm: A method for assessing and comparing underlying protein entanglement"
This notebook allows you to compute writhe and average crossing number fingerprints of smoothed representations of protein backbones. The code downloads PDB files, and smoothes the alpha-carbon backbone to a minimal representation reserving the underlying topological structure. With these writhe fingerprints, once can analyse the backbone for large scale helical structures, and compare it to a database of smoothed structures to identify similarities.
We recommend using the SWRITHE package locally with Linux or MacOS. To install, run the below in the terminal.
git clone https://github.com/arronelab/SWRITHE.git
cd SWRITHE
makeThis notebook is maintained by Arron Bale, email me at arron.n.bale@durham.ac.uk if you need any help with installation or potential new features