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I'm trying to download a list of all of the non-redundant protein chain IDs in the RSCB-PDB (not the actual FASTA entries, just the IDs), filtered by some % identity.

Does anyone know how to do this? I haven't been able to figure it out with the advanced search function .

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  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Nov 4, 2023 at 20:27
  • $\begingroup$ % identity to what? To each other? To a specific query sequence? $\endgroup$
    – terdon
    Nov 5, 2023 at 11:15
  • $\begingroup$ Please add some additional context to your question. Why dod you want to download this list? $\endgroup$
    – gringer
    Nov 5, 2023 at 11:18
  • $\begingroup$ @terdon I believe he needs the ones not identical AKA different ones ' non-redundant' as he says $\endgroup$
    – pippo1980
    Nov 5, 2023 at 12:11
  • $\begingroup$ So the ones that do not have more than X% identity to any others in the database, @pippo1980? OK, so what identity? And won't all of them be non-redundant? I mean, if they are identical, they wouldn't have a different ID, would they? (I know, my deep, deep ignorance of the protein structure field is probably evident here) $\endgroup$
    – terdon
    Nov 5, 2023 at 12:24

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Did you try RCSB sequence similarity search? These two announcement highlight the options you ask about:

Alternatively, if you'd like to calculate identity on your own, you can download sequences of all the PDB entries from: https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt (270MB).

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  • $\begingroup$ Thank you! The files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt link was what I needed. Any way to filter them by identity from the text file? $\endgroup$
    – user18494
    Nov 6, 2023 at 1:27
  • $\begingroup$ I suppose you'd need to do pairwise sequence alignment and calculate identity. $\endgroup$
    – marcin
    Nov 6, 2023 at 7:03

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