Qingyuan Feng

The SMILES format is converted to RDKit Mol object and then converted to ECFP (in this case, Morgan Fingerprint, which is nearly identical to ECFP) in this line: https://github.com/simonfqy/PADME/blob/e01c592cc06c4de04b3ed6db35da5af5ff7f863f/dcCustom/feat/fingerprints.py#L23. As...

Hi, I apologize that my code is currently a bit dirty. You're welcome to make changes, but if you don't, please do as what I say, and I will try...

Now the code is much more modularized, though there are some remaining problems in some of the scripts, which I was a bit lazy to fix and simply chose a...

I am very sorry that I did not get back to you earlier. Thank you for your kind words! The `.sh` files are independent of each other, you don't need...

Hi, if you want to predict the forces between compound molecules and protein, you should train the model using the data of forces. In my implementation, Davis, Metz, KIBA and...

Hi, I am very sorry for forgetting to update the files in the GitHub repo. This has created troubles for you. I have now updated the files including the `driver.py`...

Hi @Running-z . I am a bit confused regarding your first question. Are you using the current version of the repo? You can refer to `drive_d.sh` file for a process...

@Running-z Thanks. If you remove the `--cross_validation`, `--cold_drug`, `--cold_target` or `--split_warm` parameters from the `.sh` script like what I did for `drive_nci60.sh`, you would get the predictions for all drug-target...

@Running-z I think it is a good point. I will do this in a couple of days. It is not so straightforward as it seems, because the existing implementation follows...

@Running-z I believe I have been very patient and responsible regarding your questions and requests. If your research results in a publication, it would be very nice if you could...