[Protein-analysis] Re: pdb-l: About PDB Files and Secondary Structures

Dan Bolser via proteins%40net.bio.net (by dan.bolser from gmail.com)
Mon Jun 16 05:26:24 EST 2008


2008/4/23 Narges Habibi <narges.habibi from gmail.com>:
> Hi all,
>
> I'm doing a project on "Protein Contact Map Prediction" and I use some
> features for nueral network's input, including Secondary Structure of a
> given Amino Acid. There are several ways:
>
> 1- getting dssp file for each pdb file (from ftp server)
> 2- extracting from pdb file (The HELIX and SHEET and TURN section)
> 3- getting ss file from www.pdb.org (as I see the given sequences in this
> file don't match with the pdb files, why?)
>
> What do you suggest? What method is more accurate?

I have summarised the various replies to this and similar questions
from the archive into the PDB FAQ here:

http://pdbwiki.org/index.php/PDB_FAQ#Q:_How_do_I_find.2Fpredict.2Fdisplay_secondary_structure.3F


Comments and feedback on this summary are appreciated.

Dan.


> Thanks in advance
>
> --
> Narges Habibi
>
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