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

Dan Bolser via proteins%40net.bio.net (by dan.bolser from gmail.com)
Wed Apr 23 07:12:53 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)

This method has the advantage of giving you a consistent definition of
what is helix / sheet / turn / etc., but the disadvantage of sometimes
missing short regions of sheet in particular.

>  2- extracting from pdb file (The HELIX and SHEET and TURN section)

The problem here is that the given definitions may be inconsistently
applied, depending on the tastes of the particular PDB author. I don't
know to what extent the annotations in the PDB entries match DSSP.

>  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?)

I don't know about this method.

>  What do you suggest? What method is more accurate?

If we knew that we wouldn't have more than one method ;-)

In reality what you mean by 'accurate' varies depending on the application.

>  Thanks in advance
>  --
>  Narges Habibi
>  https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l .


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