[BiO BB] [Fwd: Extracting helix/strand sequences from pdb:]

[Indraneel Majumdar]

Hi,

There seems to be a lot of software for doing this. I guess you are
trying to extract out the secondary structure information corresponding
to each PDB file. The SHEET and HELIX headers in the PDB file itself are
quite accurate as they are generated by the DSSP program. Other programs
you may use to get similiar information are sstruc, jpred, predict
protein.
You may want to check out these pages:
http://barton.ebi.ac.uk/new/software.html
http://www.expasy.ch/tools/
http://biochem9.chem.ufl.edu/~cannaro/latex/appendix/appendix.html

You might have to write a perl script to run the program of your choice
on each PDB file and then extract out the relevant info from the output
file and write it to another taking the PDB filename as the template.
eg 1EMB.pdb -> 1EMB.ss
I could not find any script for doing this on the net.

best wishes,
Indraneel

PS: I am writing one such tool myself, which my employer shall release
as open source, but it's still some way to go.

On Mon, Apr 16, 2001 at 02:38:40PM +0000, J.W. Bizzaro wrote:
> 
>   Do anyone have a script or know of a source where I can obtain the
> sequences of helix/sheet
> from pdb file. Any help will be appreciated! 
> 

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