VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Jan 21 2008 - 10:51:11 CST

Indeed. In the very best and luckiest cases you can get an accuracy of
75% in the prediction of secondary structure motifs. However, this
would work out well for small and medium sized peptides (I've seen a
good prediction and convergence of different methods for peptides to
up to 60 residues); unfortunately, if your peptide sequence gets
longer and longer, the prediction rates start to go down. In any case,
I agree with Peter on reading more about a particular method before
trusting the results. I'd like to add that you should not only try a
single method, but at least 4 (there are plenty of them out there) so
you can get a more consensus idea on how your peptide might fold.

Cheers,
Michel

On Jan 21, 2008 5:09 PM, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> With that being said, there are many tools to attempt to do this; see,
> eg, http://ca.expasy.org/tools/#secondary; their effectiveness varies
> and I'd urge you to read up on each particular method before you trust
> the results.
> Best,
> Peter
>
>
> Axel Kohlmeyer wrote:
> > On 1/21/08, Lu Lin <llu_at_cs.hku.hk> wrote:
> >
> >> Dear VMDers,
> >>
> >> I have a non-VMD problem, but I really want your help as I have little
> >> knowledge of biology.
> >>
> >> Can we recognize the secondary structure elements such as alpha-helix
> >> simply from the sequence of a protein? Or is there any pattern or clue
> >>
> >
> > sadly, no. if that would be the case the folding_at_home
> > project and quite a few other people would be out of work.
> > ;-)
> >
> > cheers,
> > axel.
> >
> >
> >> for alpha-helix in the sequence of a protein?
> >>
> >
> >
> >> Would anyone help me? Thanks a lot!!!
> >>
> >> Best regards,
> >> Linda
> >>
> >>
> >>
> >>
> >
> >
> >
>