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

Oznur Tastan via proteins%40net.bio.net (by otastan from gmail.com)
Thu Apr 24 12:34:25 EST 2008


*The following recent article  provides a comparison:* * 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.
----
Oznur Tastan
PhD Candidate,
Computer Science Department
Carnegie Mellon University

On Thu, Apr 24, 2008 at 10:39 AM, Dan Bolser <dan.bolser from gmail.com> wrote:

> 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
> >
> >
> >
>
>
> --
> hello
>
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>



-- 
oznur


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