I am using hhpred to find matches to my peptide queries (45-50aa long) against the PDB database.
For the matching coords in the top-ranked PDB file, I want to check whether those coords correspond fully or partially to my (Pfam-defined) protein domain of interest.
How can I perform this mapping of PDB match to Pfam domain name in a high-throughput manner at the command line?
I realize there are links to 3rd party tools for parsing the PDB files (http://bit.ly/1JcsSt6), but I've never played around with PDB files, so I thought I might first glean ideas from the helpful forum members here. If you think I could ask this question in another forum more qualified to answer this question, I would appreciate that as well. Thank you!