jhmlam/allosteric-pathways

Building and analyzing residue interaction networks with cofactors (includes tutorial).

This repository contains a jupyter notebook tutorial together with the necessary information and code for extracting allosteric pathways in proteins, including multimeric proteins and protein complexes.

The calculations can also be done via command line as demonstrated in example_protein_cofactor_network_analysis.sh.

Dependencies:

• Python 3.6
• Scikit-learn 0.19 or later
• Scipy 1.3.0
• Matplotlib
• Mdtraj: http://mdtraj.org/1.9.3/
• Biopandas: http://rasbt.github.io/biopandas/
• LAPJV (for lipid-protein networks): https://github.com/gatagat/lap

See tutorial for more information.

Citing this work
The code and developments are described in two papers.

[1] P.W. Kang, A.M. Westerlund, J. Shi, K. MacFarland White, A.K. Dou, A.H. Cui, J.R. Silva, L. Delemotte and J. Cui. Calmodulin acts as a state-dependent switch to control a cardiac potassium channel opening. 2020

[2] A.M. Westerlund, O. Fleetwood, S. Perez-Conesa and L. Delemotte. Network analysis reveals how lipids and other cofactors influence membrane protein allostery. 2020

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Annie Westerlund, KTH Royal Institute of Technology, 2020