Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark Cancer Systems Biology, Health and Technology Department, Section for Bioinformatics, 2800, Lyngby, Denmark
PyInKnife2 is a set of Python scripts to run an updated version of the PyInKnife pipeline [1] for Protein Structure Network (PSN) analysis using PyInteraph2 [2].
When using PyInKnife2 and PyInteraph2 for publication, please cite:
Valentina Sora, Matteo Tiberti, and Elena Papaleo, PyInteraph2 and PyInKnife2 to analyze networks in protein structural ensembles, bioRxiv, https://doi.org/10.1101/2020.11.22.381616
Please see the INSTALL.md file for instructions on installing PyInKnife2.
We provide a detailed user guide inside the doc/ directory and a step-by-step tutorial inside the tutorial/ directory.
[1]: Viloria, Juan Salamanca, et al. "An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass." Scientific reports 7.1 (2017): 1-11. [2]: Tiberti, Matteo, et al. "PyInteraph: a framework for the analysis of interaction networks in structural ensembles of proteins." Journal of chemical information and modeling 54.5 (2014): 1537-1551.