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cgoliver / RNAmigos

GCN implementation for RNA-small molecule binding prediction. (https://academic.oup.com/nar/article/48/14/7690/5870337)
http://rnamigos.cs.mcgill.ca
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Construct training data from scratch #8

Closed JasonJiangs closed 7 months ago

JasonJiangs commented 7 months ago

Hi RNAmigos team,

Thanks for developing this great tool. I am trying to train this model on my own data. I am wondering is there the entrance for my to obtain the parsed the annotated pocket data (pockets_nx_symmetric_orig) given the pdb id and pocket information?

Thanks!

cgoliver commented 7 months ago

Hello @JasonJiangs ,

Thank you for your interest in RNAmigos!

May I ask, are the PDBs you are interested publicly available on the RCSB databank?

Best, Carlos

JasonJiangs commented 7 months ago

Hello @JasonJiangs ,

Thank you for your interest in RNAmigos!

May I ask, are the PDBs you are interested publicly available on the RCSB databank?

Best, Carlos

Dear Dr. Oliver,

The PDBs I am using to construct the training data are publicly available on the databank.

Best, Jason

cgoliver commented 7 months ago

Hi Jason,

In that case it should be fairly straightforward to use the graphs provided by rnaglib to train a new model.

@jgcarvajalp created a pull request do just that since rnaglib did not exist when RNAmigos was first released.

It would be great if you test it out and let us know if you run into any issues, and then we can merge the PR.

I'm going to close this issue and we can move the conversation to #5 so that Juan can help out.

Best, Carlos