luost26/3D-Generative-SBDD

How to test the program by our own system

YuxiuLiu opened this issue · 4 comments

YuxiuLiu commented

Sorry to bother you，I ran the test model successfully and got the smiles structures of generated molecules, however, I have no idea about how to run our own example, though we replace the test system with our own one and I also wonder the meaning of the number in the last part of this list ('YPKA_YERPS_90_433_0/5ce3_B_rec_5ce3_adp_lig_tt_min_0_pocket10.pdb', 'YPKA_YERPS_90_433_0/5ce3_B_rec_5ce3_adp_lig_tt_min_0.sdf', 'YPKA_YERPS_90_433_0/5ce3_B_rec.pdb', 0.552965)

luost26 commented

Hi!

We are planning to release a script that can convert other proteins to the model-supported format.

  • YPKA_YERPS_90_433_0/5ce3_B_rec.pdb: is the path to the target protein's PDB file.
  • YPKA_YERPS_90_433_0/5ce3_B_rec_5ce3_adp_lig_tt_min_0_pocket10.pdb: is the path to the extracted pocket, a substructure of the protein.
  • YPKA_YERPS_90_433_0/5ce3_B_rec_5ce3_adp_lig_tt_min_0.sdf: is the path to the reference ligand.

All of them can be found in the unprocessed dataset archive: crossdocked_pocket10.tar.gz.

  • 👍1
YuxiuLiu commented

Hi!

We are planning to release a script that can convert other proteins to the model-supported format.

  • YPKA_YERPS_90_433_0/5ce3_B_rec.pdb: is the path to the target protein's PDB file.
  • YPKA_YERPS_90_433_0/5ce3_B_rec_5ce3_adp_lig_tt_min_0_pocket10.pdb: is the path to the extracted pocket, a substructure of the protein.
  • YPKA_YERPS_90_433_0/5ce3_B_rec_5ce3_adp_lig_tt_min_0.sdf: is the path to the reference ligand.

All of them can be found in the unprocessed dataset archive: crossdocked_pocket10.tar.gz.

Sorry to bother you again, what's the meaning of the number 0.552965 in the list?

luost26 commented

Hi!
We are planning to release a script that can convert other proteins to the model-supported format.

  • YPKA_YERPS_90_433_0/5ce3_B_rec.pdb: is the path to the target protein's PDB file.
  • YPKA_YERPS_90_433_0/5ce3_B_rec_5ce3_adp_lig_tt_min_0_pocket10.pdb: is the path to the extracted pocket, a substructure of the protein.
  • YPKA_YERPS_90_433_0/5ce3_B_rec_5ce3_adp_lig_tt_min_0.sdf: is the path to the reference ligand.

All of them can be found in the unprocessed dataset archive: crossdocked_pocket10.tar.gz.

Sorry to bother you again, what's the meaning of the number 0.552965 in the list?

Hi

Can you provide to context of the number 0.552965? Thanks!

luost26 commented

Hi,

Now you may use sample_for_pdb.py to generate ligands for your proteins. Instructions and examples are in the README.