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patrickbryant1 / SpeedPPI

Rapid protein-protein interaction network creation from multiple sequence alignments with Deep Learning
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Does the used version of AF provide .sc files #17

Closed KoussaiB closed 5 months ago

KoussaiB commented 5 months ago

Hello,

Thanks for this great tool!

I have question regarding the output,

I was wondering if we can edit the used alphafold model in this tool to also generate an .sc file in order to be able to filter with pae_interaction <10 as in https://github.com/nrbennet/dl_binder_design

The thing is, I am running this tool as a part of an in-silico binder design pipeline and wanted to check if I can integrate this scoring function as apart of the output.

Best and thank you in advance!

patrickbryant1 commented 5 months ago

Hi,

There is no PAE in this version of AF (this is the original).

If you want to design binders, see : https://github.com/patrickbryant1/EvoBind

Hope this helps!

Patrick

KoussaiB commented 5 months ago

will try that, thank you for your help!