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

Dan Bolser via proteins%40net.bio.net (by dan.bolser from gmail.com)
Thu Apr 24 09:39:40 EST 2008


On 23/04/2008, Pooja Jain <pcxpj1 from nottingham.ac.uk> wrote:
> Hi Dan,
>
>
>
> >
> > >
> > > 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.
> >
> >
>
>  Which region do you mean DSSP might miss ?  The terminal ends of the
> strands in a sheet, the terminal strands of the sheet or perhaps the
> interrupted strands in a sheet ?
>
>  Would you please share further details, any statistics or any reference
> that discusses these missing regions please ?

I am glad you brought this up, because the truth is that I don't
really know! I have only ever heard this said - I have not seen any
statistics or examples. It would be great to get more information from
the list about the identification (and validity) of short regions of
secondary structure.

Sorry for any confusion,

Dan.

>
>  Many thanks,
>
>  -Pooja
>
>
>


-- 
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