I have an XML output file from BLAST, how to find matches in the PDB Database?

Question

I have an blast output XML file and I want to find a way to run the contents of the file through the RSCB Protein Data Bank in order to find some kind of homology between my output file and anything in the PDB using Python.

I'm still new to all of this and am stumped as to go about starting this. Thanks in advance!

Answer 1

Could you give a sample of your BLAST output?

Have you already taken a look at this page?

http://www.rcsb.org/pdb/software/static.do?p=/software/webservices/search_nmr.jsp

It should help you get started with using their API.