PDB -> SwissPROT conversion?

Paul Davis Paul at pdchem.demon.co.uk
Fri Jun 5 10:58:16 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 program STRIDE by Frishman and Argos, which I obtained


will generate secondary structure assignments from the
atomic coordinates in a PDB file.  While the assignments
will not always correspond exactly to the HELIX, SHEET and
TURN records of a PDB file (where these are present), they
are made in a consistent manner and are possibly more useful
in comparative studies.

STRIDE can also output the sequence in fasta format.

See Proteins 23: 566-579 (1995)


Paul Davis                                   paul at pdchem.demon.co.uk

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