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2 hours ago by

Hi. How may I find "Identical Protein Groups" from PDB database using commandline? So far, I have been using the following command, which successfully grabs the primary PDB but unfortunately does not include "Identical Protein Groups", aka "Related Structures":

blastp -query fasta_file -out output.blast -evalue 1e-60 -db pdbaa -num_threads 4 -outfmt 7

For example, www.rcsb.org/structure/5WFL is has the following "Primary Citation of Related Structures:"
5WFV, 5WFL, 5WG1, 5WHO, 5WHL, 5WIY. (all 7 structures are from one manuscript).

My blastp command only picks-up one of these PDB codes. How can this commandline be adjusted to include ALL 7 PDB codes?



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