Blast Search PDB

Blast Protein Data Bank for structures matching a user given sequence.

prody_blast(sequence, **kwargs)[source]

Blast search PDB and download hits.

  • sequence – sequence or file in fasta format
  • identity (float) – percent sequence identity for blast search, default is 90.0
  • overlap (float) – percent sequence overlap between sequences, default is 90.0
  • outdir (str) – download uncompressed PDB files to given directory
  • gzip – write compressed PDB file

Blast Parameters

  • filename (str) – a filename to save the results in XML format
  • hitlist_size (int) – search parameters, default is 250
  • expect (float) – search parameters, default is 1e-10
  • sleep (int) – how long to wait to reconnect for results, default is 2 sleep time is doubled when results are not ready.
  • timeout (int) – when to give up waiting for results. default is 30