[Protein-analysis] About PDB Files and Secondary Structures

Oznur Tastan via proteins%40net.bio.net (by otastan from gmail.com)
Wed Apr 23 16:00:05 EST 2008


Hi Narges,
I recommend to have a look at the following article for comparison of
different methods and for other secondary structure assignment methods that
you have not listed:
*Zhang W, Dunker AK, Zhou Y.**Assessing secondary structure assignment of
protein structures by using pairwise sequence-alignment benchmarks, *
Proteins. 2008 Apr;71(1):61-7.
Different methods would  success and fail at different cases, I would build
the model by incorporating multiple method's assignments.
Hope that helps,
Oznur Tastan

On Wed, Apr 23, 2008 at 7:25 AM, Narges Habibi <narges.habibi from gmail.com>
wrote:

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



-- 
oznur


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