pre-trained model

[msako82]

I'm very interested in your job.
I downloaded the source code, but I can not download the pre-trained unconditional VAEs model.
The file does not exist. Could you please upload it again?

Or, I would like to sample ligand for a specific PDB file, can you provide a learned model?

[nnkhang19]

Hi,

Thanks for reaching out. We apologize for your inconvenience. As we have updated the code with more experiments on the PDBBind dataset, I just uploaded several new files and checkpoints of our models. Please check the checkpoint folder, where you can find some checkpoints, including the pre-trained unconditional VAEs and the fine-tuned model on the PDBBind dataset (target-aware.pt). Additionally, the pdb files used in our study are stored in the pdb folder.

[msako82]

Thank you so much for your job!
I will try to use target-aware.pt.
In the generate_with_specific_target.py code, checkpoint file is set to "checkpoint/target_aware.pt".
Is it correct that the ligand sampling can be done with fine tuned models in the PDBBind dataset by using the following?
python3 generate_specific_target.py --protein_name [target name]

[msako82]

I tried to use generate_specific_target.py, but I can not import "get_esm".
I looked for how to install "get_esm" but could not find it. Is this your own function? Do you have the source code?

[nnkhang19]

Hi @msako82, I apologize for the late response. I had some deadlines to finish in April and May. Now, I just uploaded the "get_esm.py" to the repository. Now, you can rerun the code with this file. Thank you for considering our work. Please let me know if there are any further issues.