search

dauparas / ProteinMPNN

Code for the ProteinMPNN paper
MIT License
934 stars 284 forks source link

How to get the predicted PSSM from structure? #39

Closed bzhousd closed 1 year ago

bzhousd commented 1 year ago

Dear ProteinMPNN team,

Thank you for building such fantastic method to generate sequences from structure. I am thinking of getting a PSSM logo from a known structure. how can I get the predicted PSSM from a structure?

After I checked the code, it looks like I can use log_probs in this line , and I also need to run this many times(not sure how big to be converged ) because ProteinMPNN decoder is in random decoding order. is this correct?

Thank you for your helps in advance

dauparas commented 1 year ago

Hello! You can get the PSSM-like predictions using --unconditional_probs_only 1 flag.