PDB -> SwissPROT conversion?

Iddo Friedberg idoerg at cc.huji.ac.il
Sun Jun 7 02:02:04 EST 1998


Al Wang wrote:
> 
> 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.
> 


I'd just like to add a comment which might be relevant in this case: PDB
residue numbering is, at times, non-consecutive, or may contain
non-numeric characters (e.g. 31A). This may cause problems if somehow
you wish to later correlate your sequence file with the PDB file.

I recommend using DSSP, and then running a script on the resulting DSSP
file. That way you preserve PDB residue numbering, consecutive
numbering, and 2ndary structure.

About DSSP:
http://www.sander.embl-heidelberg.de/dssp/


Iddo


-- 
Iddo Friedberg
Phone: (972)-2-6758647
email: idoerg at cc.huji.ac.il
web: http://www.ls.huji.ac.il/~idoerg
More info: finger idoerg at cc.huji.ac.il




More information about the Bio-soft mailing list