PDB -> SwissPROT conversion?

Andrew Martin amartin at stagleys.demon.co.uk
Sun Jun 7 17:20:52 EST 1998


Catherine  Letondal (letondal at pasteur.fr) wrote:


: In article <6l7588$j4n$1 at netnews.upenn.edu>, alwang at blue.seas.upenn.edu (Al Wang) writes:
: >Hi,
: >
: >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.  
: >
: >Thanks,
: >Al

: I am looking for the same kind information. There is a description of a program called
: PDB2PIR on the PIR Web (see http://nbrfa.georgetown.edu/pir/software.html)
: but it has not been put on their ftp server.
: I am waiting for an answer from the author of the program (Dr. John S. Garavelli, 
: Associate Director of PIR).

I have a pdb2pir program which anyone is welcome to a copy of. It
is moderately intelligent and can read from just the ATOM records
or optionally include information from the SEQRES records as well.
Note this is PIR output and not SwissProt as originally requested
so there's certainly no feature information!

Please EMail me if you are interested - either by replying to this
posting (my home address) or at martin at biochem.ucl.ac.uk

Best wishes,

Andrew






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