Optimal Path correlation

[Aiswarya Pawar]

Dear Bio3d Team,

So I have been succcessfully able to point out the path regulating the allostery in my protein. And with the help of cnapath command, i can get optimal and sub-optimal paths.

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 pa <- cnapath(net, from=10, to=100, k=500)

But I want to see the degeneracy value of individual path. For example if i do

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pa$path[[1]]

it displays the residues in the path one, and so on. I assume the number is irrespective of the shortest path.

Is there someway i can get the first 5 paths degeneracy values or can i get first 5 paths that are relevant based on their shortest path.

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Also, is there a way to increase the thickness of the spline for viewing in VMD?.

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Thank you

[Xinqiu Yao]

Hi,

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I am not very clear about your first question. If what you want is to calculate the ‘node degeneracy’, the function summary()can help (see ?summary.cnapath for more detail).

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About the second question, the thickness of spline is scaled by the path length and the max thickness is (unfortunately) hard coded in the released version of Bio3D. One way to solve it is to “hack” the code and change the magnitude manually. For example, type vmd.cnapath ← edit(vmd.cnapath). Find the line with r = rad(x$dist[j], rmin, rmax, radmax = 0.1) (around line #112). Change radmax = 0.1 to a larger value, e.g., 0.5. Then quit the Editor. There will be a modified function in your Workspace named ‘vmd.cnapath’. Use that function to draw paths. Note that the modified function only exists in your current R session. To save it for future use, save(vmd.cnapath, file=”myfun.RData”. To load it, load(“myfun.RData”).

[Aiswarya Pawar]

What I meant by first question, so we do have some n paths from the cnapath command stored in pa.

The paths in pa have optimal and suboptimal paths? But how do I know what are the residues in the shortest path in ascending order. Let say if I want to see 5 shortest path it takes to from source to sink.

Eg : A- B-C-D

A-F-C-E-D

A-G-F-C-E-D

In this first can be the shortest and the rest path be preceding paths which are also possible path a protein can take?

Summary can give us a single path and their node degeneracy but same way can we have all possible suboptimal paths? So that we can correlate all the paths.

[Xinqiu Yao]

The “paths” in a cnapath object (e.g., your pa) contain optimal/shortest and suboptimal (still very short but slightly longer than the shortest) paths. Normally, the first is the shortest path. The order of paths are based on their distances (which are saved in pa$dist).

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‘Node degeneracy’ stands for the number of suboptimal paths going through that node (and is divided by the total number of paths if normalized). Therefore, there is no node degeneracy for a ‘single path’. The result you obtained from ‘summary()’ is a statistics over all optimal/suboptimal paths in pa$paths.

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Hope it may help.