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How to retrieve representative at 30% sequence identity in PDB

I plan to use the PDB advanced search to filter sequences. I need to create a test set of protein sequences. The selection conditions are probably chain length, resolution, macromolecule type, etc., which are all easy to implement.

But there is another restriction: retrieving representative at 30% sequence identity. How do I achieve this?

pdb
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updated by GenoMax GenoMax • written by bosimiya • bosimiya

1 answer

First you download a FASTA file with all PDB sequences.

Next you cluster them down to 30% identity using MMseqs2.

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written by Mensur Dlakic Mensur Dlakic

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