Which parameters to use? #11
Description
Hey Philip,
Thanks a lot for creating this tool, I am currently looking into how I can best put it to use!
I have a question related to the AF parameters that are used. As seen in your colab notebook, you either use the parameter files model_2_ptm or model_2_ptm_ft4.
Am I correct in guessing that the model_2_ptm file are the normal AF multimer parameters and the model_2_ptm_ft4 are the fine-tuned parameters which were also used in the paper? Or are they fine-tuned in a different way?
And which parameters would you recommend for a discrimination task and which ones for simple structure prediction? In #10 you mentioned that the fine-tuned actually performed worse for decoy discrimination.
When using the --new_docking flag, should only certain parameters be used?
Thank you and kind regards,
Elias