What is it about?
Residues in biomolecules (proteins, DNA, complex glycans) interact with each other forming an interaction network. Much like in road, computer or social networks, certain nodes are dominant in the "communication" within the network. These have to be discovered by some network algorithms. pyProGA is a PyMOL plugin with such functionality. You can study simple distance based networks, or perhaps more revealing, interaction energy based networks.
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Photo by National Cancer Institute on Unsplash
Why is it important?
This method allows to identify central residues that play crucial roles in e.g. binding of two (or more) biomolecules (e.g. proteins) into complexes - such processes are indispensable for molecular communication inside and between cells. Much of our immune system is based on such communication and recognition between the "right" ligand-host pairs. Several diseases, including viral attacks, exploit these mechanisms by mimicking natural binding partners. Subtle differences can be analysed by this tool presented in the paper.
Perspectives
I hope that this paper can ad one more arrow into the quiver of methods used in molecular biology by making this somewhat technical/theoretical method readily available to end users. The goal was to place it, so to speak, at your fingertips. Critical comments and suggestions are of course welcome. Check it out at https://gitlab.com/Vlado_S/pyproga
Vladimir Sladek
Institute of Chemistry, Slovak Academy of Sciences
Read the Original
This page is a summary of: pyProGA—A PyMOL plugin for protein residue network analysis, PLoS ONE, July 2021, PLOS,
DOI: 10.1371/journal.pone.0255167.
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