Abstract
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.
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Acknowledgments
This work is supported by NIH Grant R01-GM130834. Computational resources were provided via the Extreme Science and Engineering Discovery Environment (XSEDE) allocation TG-MCB160119, which is supported by NSF grant number ACI-154862.
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Botello-Smith, W.M., Luo, Y.L. (2021). Concepts, Practices, and Interactive Tutorial for Allosteric Network Analysis of Molecular Dynamics Simulations. In: Schmidt-Krey, I., Gumbart, J.C. (eds) Structure and Function of Membrane Proteins. Methods in Molecular Biology, vol 2302. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1394-8_17
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DOI: https://doi.org/10.1007/978-1-0716-1394-8_17
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