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rdk / p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.
https://rdk.github.io/p2rank/
MIT License
234 stars 31 forks source link

Pocket Volume Estimations #68

Open apl22 opened 4 months ago

apl22 commented 4 months ago

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 commented 4 months ago

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?

apl22 commented 4 months ago

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!