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zshuyinggg / ppi_mutation

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Isoforms #6

Open zshuyinggg opened 1 year ago

zshuyinggg commented 1 year ago

In the file huintaf2-main/data/HuRI-uniprot-mapping.csv

There are many mappings that mapped the ensemble to isoform-2 of a protein, e.g. ENSG00000072682,O15460-2

However, in the file HuRI-merged-allnames.csv, there is no isoform specified for every protein-protein interaction: 542509,O15460-Q13643,ENSG00000072682,ENSG00000183386,6EVL;6EVM;6EVN;6EVO;6EVP;,1WYH;2CUQ;2EHE;,O15460,Q13643,ENSG00000072682-ENSG00000183386,O15460-Q13643

zshuyinggg commented 1 year ago

need to know what structure/sequence they used to predict the complexes

zshuyinggg commented 1 year ago

In their predicted complexes folder: ENSG00000072682-ENSG00000183386, we can only find: ENSG00000072682-ENSG00000183386.overlap ENSG00000072682-ENSG00000183386.pdb ENSG00000072682-ENSG00000183386.pLDDT

Can we know the original structure used for each protein from these files? I also pulled out the description in their paper as below:

image

which i don't fully understand if they mentioned anything about the isoform

zshuyinggg commented 1 year ago

I found out a ENSG00000072682.pdb in the folder: Huri-single And I converted it to fasta, turned out they used ISOFORM 1 instead of ISOFORM 2