[Protein-analysis] About PDB Files and Secondary Structures

[Narges Habibi]

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