PDB -> SwissPROT conversion?
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
o Immunoglobulin and other entries that SWISSPROT excludes to avoid
o new PDB entries that have not yet made it into SWISSPROT or SWISSNEW
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