Concepts, Practices, and Interactive Tutorial for Allosteric Network Analysis of Molecular Dynamics Simulations.

Over the past decade, concepts of network theory in combination with dynamical information from conformational ensembles have been widely applied to gain insights in understanding allosteric regulation in biomolecules. In this chapter, we introduce the basic theories and protocols used in protein dynamics network analysis through a series of interactive python Jupyter notebook scripts. While various network analysis methods exist in the literature, here we focus on the two popular methods based on correlated atomic motions and pairwise interaction energies. While the tutorial is based on a small prototypic protein, the workflow and protocol introduced here are optimized to handle large membrane proteins.