Ligand_Generation pre-trained model

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?

Mar 17 '24 01:03 msako82

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.

Mar 18 '24 08:03 nnkhang19

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]

Mar 18 '24 09:03 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?

Mar 19 '24 05:03 msako82

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.

May 17 '24 10:05 nnkhang19