Community network analysis

Regarding the community network analysis, we largely followed the instructions outlined in the tutorial below provided by the Luthey-Shulten Group:

https://luthey-schulten.chemistry.illinois.edu/tutorials/network/network_tutorial.pdf

The tutorial also covers the visualization of the network on a 3D molecular structure using VMD. This tutorial provides the best protocol for the community network analysis we performed in the paper.

For additional information, please refer to these references:

1) A. Sethi, J. Eargle, A. A. Black, Z. Luthey-Schulten, Dynamical networks in tRNA:protein complexes. Proc. Natl. Acad. Sci. U.S.A. 106, 6620–6625 (2009).

https://doi.org/10.1073/pnas.0810961106

2) John Eargle, Zaida Luthey-Schulten, NetworkView: 3D display and analysis of protein·RNA interaction networks, Bioinformatics, 28, 22, 3000–3001, (2012). 

https://doi.org/10.1093/bioinformatics/bts546

3) W. Humphrey, A. Dalke, K. Schulten, VMD: Visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).

https://doi.org/10.1016/0263-7855(96)00018-5