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aqlaboratory / openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
Apache License 2.0
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How to emphasize on the structure? #463

Open bzhousd opened 3 months ago

bzhousd commented 3 months ago

Thank you for this great work. I learned a lot of insights of alphafold from openfold paper.

I am predicting antibody-antigen complex. In my case, I already know the structure of Ab-Ag complex, I generated some mutants from this Ab-Ag(say <10 mutations in CDR), now I want to predict the structures of mutants. I found alphafold doesn't use template, because the output structure of alphafold is far away from template. I searched the options in run_pretrained_openfold.py, I didn't find such option to make openfold to emphasize on template? I wonder if you have a way to emphasize on initial pair-embedding when pair-embedding and single embedding are merged.

Thanks in advance

bzhousd commented 3 months ago

I found thread_sequence.py, I am not sure if it is the right tool for my mutants prediction. I read the code of thread_sequence.py, I didn't figure out how runmodel method emphasizes on template, I must miss something.