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,
On Wed, Apr 23, 2008 at 7:25 AM, 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?
>> Thanks in advance
> Narges Habibi
> Proteins mailing list
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