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Finding homologous sequences that have crystal structures

As the title says, how do I find homologous sequences that also have crystal structures? My initial thought was to blast my sequence and then manually searching for the sequence in the PDB database for crystal structures, however I was wondering if there was an automated approach so i don't have to look 100s of sequences up.

Thanks!

proteins genes sequences homologs blast
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updated by Dunois • Dunois • written by Hansen_869 • Hansen_869

I'm guessing what you need is the Foldseek server. You can search with both structures as well as FASTA sequences. Just select the PDB100 database, and that should give you hits against crystal structures.

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written by Dunois • Dunois

1 answer

I hope you don't take this the wrong way: you would be getting more responses to your questions if you made an effort to provide more details. Find homologous sequences to what?

A list of all sequences (protein, DNA and RNA) with PDB structures is updated weekly:

https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt

You can BLAST any protein sequence of interest against this database.

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written by Mensur Dlakic Mensur Dlakic

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