Request for original PDBbind & Pafnucy checkpoints

[DynaX-C]

Hi, I noticed that the repo only provides models trained on the CleanSplit dataset; would it be possible to also share checkpoints trained on the original PDBbind training set, as well as the Pafnucy checkpoint, since I’d like to run a benchmark comparison?

[DavidGraber]

Hi DynaX-C
Sorry for the delay in responding, I was out-of-office for a couple of weeks.
If this is still relevant, I can send you the GEMS checkpoints of the models trained on the full PDBbind. Which versions would you like to have? With all language models, including ESM, Ankh and ChemBERTa? I should also be able to find the Pafnucy Checkpoint.

[DynaX-C]

Hi!
No worries at all, thanks for getting back to me.
Yes, still relevant! If you could share the GEMS checkpoints trained on the full PDBbind, that’d be great. I’d prefer the versions with all the language models (ESM, Ankh, and ChemBERTa), if available.
And if you can also dig up the Pafnucy checkpoint, I’d really appreciate it!

[DavidGraber]

Sure, you can find the GEMS checkpoints attached. The Pafnucy checkpoints are much larger, you best download them from here. For training on the full PDBbind, you will need the "c0" folders. There are five because of the 5-fold CV. In each folder there are some checkpoints named best, which must be the final checkpoints.

GEMS_chkp_full_pdbbind.tar.gz

[DynaX-C]

Got it, thank you so much for sharing the files and the clear instructions!
I really appreciate your help.