Peptide Discovery

[shahik]

Hi,
thanks for the code. How can I generate only peptides (smaller proteins) using transfer learning, can I finetune (valid_data) on peptides or is there some tweak etc? thanks!

[JoshuaMeyers]

Hey @shahik, sounds like an interesting project. GuacaMol is a benchmark suite for comparing small molecule generators, while the baseline methods we provide can be tweaked in the direction of peptides. This is out of scope for our repository, however for a simple specialised approach see: https://joss.theoj.org/papers/10.21105/joss.01992.

[shahik]

Hi,
I have used this repo and it produces smaller proteins. Limitations include the validity of proteins, it's very poor as I was able to convert only 2 valid pdb structure from generated smiles. 2nd it's not suitable for peptide bonds discovery. 3rd Transformers have taken over RNNs!