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phbradley / alphafold_finetune

Python code for fine-tuning AlphaFold to perform protein-peptide binding predictions
Apache License 2.0
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Interpretation of output files #3

Open MeiMunick opened 1 year ago

MeiMunick commented 1 year ago

Hi, thanks so much for your great work! I follow the instruction to predict HLA-A*02:01 10mer binding with fine-tuned params, and finally there is a output file named polg_test2_final.tsv. I am wondering what exactly is the col.name (as follow) in this list refer to?

model_2_ptm_ft_plddt
model_2_ptm_ft_pae
model_2_ptm_ft_plddt_0
model_2_ptm_ft_pae_0_0
model_2_ptm_ft_pae_0_1
model_2_ptm_ft_plddt_1
model_2_ptm_ft_pae_1_0
model_2_ptm_ft_pae_1_1

Besides, is there any empirical cutoff value could provide to decide binding or not? Thanks for your help!