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plinder-org / plinder

Protein Ligand INteraction Dataset and Evaluation Resource
https://plinder.sh
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System ID `8q5i__1__1.GA__1.ZB` missing DNA complex #61

Open danielzeng-gt opened 2 months ago

danielzeng-gt commented 2 months ago

Dear Plinder Authors,

I have a quick question regarding the system files. I was reviewing the system 8q5i__1__1.GA__1.ZB, but I noticed that the DNA complex seems to be missing from both the system.cif and receptor.cif files. Could you confirm if this is expected?

Thank you for your help, I've attached a photo below:

Screenshot 2024-09-13 at 11 29 25 AM
OleinikovasV commented 2 months ago

@danielzeng-gt , thanks a lot for bringing this to our attention! Although there is a direct interaction between the ligand and the protein lysine sidechain - it is missing the critical context of DNA that makes interactions with both. We will fix this bug in the future release.

In the meantime, you could consider using annotations of system_num_interactions - to filter our entries that have less than a satisfactory number of interactions (the above case has 1).

We will come back with further updates!