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Pocket Volume Estimations #68

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apl22 opened this issue Feb 23, 2024 · 2 comments
Open

Pocket Volume Estimations #68

apl22 opened this issue Feb 23, 2024 · 2 comments

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@apl22
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apl22 commented Feb 23, 2024

Hi,

On the webserver there's an easy way to create a task which calculates the volumes of predicted pockets from P2Rank. Is there a way to run these tasks from the CLI? I've got a population of proteins with predicted pockets that I can't submit all to the webserver for.

Thanks!

@rdk
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rdk commented Mar 7, 2024

Hi,
unfortunately this is not possible at the moment. The volume calculation you see on prankweb.cz is actually done in the browser and is not part of P2Rank. A quote from the author:

The pocket volume is calculated by taking the atom coordinates from Mol* and then computing the convex hull of these atoms (I'm using an library for this). Everything is basically in this piece of code: https://github.com/luk27official/prankweb/blob/main/frontend/client/tasks/client-atoms-volume.tsx
The theory behind this is explained here: http://chenlab.ece.cornell.edu/Publication/Cha/icip01_Cha.pdf

I am considering implementing a pocket volume calculation estimate into P2Rank. It would be an optional function and it would probably make the prediction several times slower. Also, it would be based on a different algorithm than the one in PrankWeb. Would it be useful to you?

@rdk rdk added the question label Mar 7, 2024
@apl22
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apl22 commented Mar 8, 2024

Hi,

No worries, thanks for letting me know I'll take a look at the code. Pocket volume calculation would definitely be useful to me, please let me know if you implement it!

Thanks!

@rdk rdk added the enhancement label Jul 2, 2024
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