cnapath calculation

[胡廷予]

I am using the pa <- cnapath command to calculate residue signal pathways. I would like to ask everyone for advice on how to choose the 'from' and 'to' residues and how to determine the starting and ending points of the signal. Additionally, since cnapath calculates paths based on nodes, I am interested in learning how to project these paths onto residues. This would help me identify which amino acids the paths pass through. Thank you all for your assistance!

[Xinqiu Yao]

Hi,

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The from/to residues are dependent on the system. Usually, if you are looking at the allosteric mechanism, the residues should be one at the active site and the other at the allosteric site. To project paths to nodes, you can look at ‘node degeneracy’ values. Please see the tutorial for more detail. You can also read the following papers for references:

http://pubs.acs.org/doi/abs/10.1021/ct4008603

http://www.jbc.org/content/291/9/4742.abstract

https://pubs.acs.org/doi/10.1021/acs.jctc.1c00669

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