How to make mhc2 peptide target_to_template_alignstring file when core pep does not determined?

phbradley / alphafold_finetune

Python code for fine-tuning AlphaFold to perform protein-peptide binding predictions

Apache License 2.0

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Open HonglanLi opened 6 months ago

HonglanLi commented 6 months ago

Hi,

I really want to know how to make mhc2 peptides'

target_to_template_alignstring file

when core peptide does not determined?

Do I have to make all kinds of 11-residue subpeptides?