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Layne-Huang / PMDM

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How to sample small molecules for a specific pocket in a PDB file？ #25

Open Yuhan-Fei opened 5 months ago

Yuhan-Fei commented 5 months ago

Hi Dr. Huang

Thank you for your great work.

If I want to sample small molecules for a specific pocket of a protein, how should I use the script of sample_for_pdb.py？ Currently, sample_for_pdb.py only seems to be able to sample whole proteins, or use split_pocket_ligand.py to get known pockets where small molecules are known to bind.

Best, Yuhan

Layne-Huang commented 5 months ago

Hi Yuhan,

May I know if there is any specific error of using sample_for_pdb.py for sampling? You could just use the pdb file of the specific protein pocket for this script.

Yuhan-Fei commented 5 months ago

Hi Dr. Huang,

Thank you for the reply, I will test this method according to your suggestions

Another question is I noticed that the loss is around 700 after 500 epoch based on the whole crossdocked dataset, and I found the reason for this large loss value is mainly due to the loss_pos (especially contribute by loss_pos_local), I don't know if you've noticed this in your previous training or do you think this loss is normal?

I am looking forward your reply.

Best, Yuhan