PDB -> SwissPROT conversion?

Peter Rice pmr at sanger.ac.uk
Fri Jun 5 09:54:58 EST 1998


In article <6l7588$j4n$1 at netnews.upenn.edu>, alwang at blue.seas.upenn.edu (Al Wang) writes:
> >Does anyone know what's a good way to take a Brookhaven PDB file, extract 
> >the sequence information, and save it in SwissPROT format?  If it can 
> >also extract the secondary structure features, even better.  

The simplest is to look in SWISSPROT. You will find the sequence (complete
even if the PDB entry is a fragment) and the secondary structure assignments.

Of course, there are cases where this does not apply:

o more than one structure for a protein, where SWISSPROT may have only one
  example

o Immunoglobulin and other entries that SWISSPROT excludes to avoid
  redundancy

o new PDB entries that have not yet made it into SWISSPROT or SWISSNEW





More information about the Bio-soft mailing list