modelling protein structPRINTures

ewan birney birney at molbiol.ox.ac.uk
Mon Jan 30 13:29:50 EST 1995


sali at tamika.rockefeller.edu (Andrej Sali) wrote:
>
> In article <3gbenc$and at mserv1.dl.ac.uk> <bionet at cgmvax.cgm.cnrs-gif.fr>  
> writes:
> > >
> > >This is much too pesimistic. About one third of all currently known
> > >sequences are related to at least one currently known structure. 
> > >
> > 
> > ??? You really mean that 15,000 sequences from Swissprot (for example)  
> are 
> > related to at least one entry in the PDB ? I'd be interested in getting  
> a 
> > reference on this subject.
> > 
> > Cheers,
> > 
> > Jean-Loup
> > 
> > 
> >    ---------------------------------------------------------------------
> >   Jean-Loup Risler                      Tel:  (33 1) 69 82 31 34
> >   CNRS		                        Fax:  (33 1) 69 07 49 73
> >   Centre de Genetique Moleculaire	Email:  
> risler at cgmvax.cgm.cnrs-gif.fr
> >   91198 Gif sur Yvette Cedex  France    
> >    ---------------------------------------------------------------------
> > 
> > 
> 
> I have not meant exactly what you said, because I wanted to be  
> conservative, but it is close enough. Many of the actually related  
> sequence-structure pairs cannot be detected as such (yet) because the  
> usual sequence alignments and even threading techniques are not perfect  
> (yet). You can get the hard numbers in the very nice paper by Orengo,  
> Jones, Thornton, Nature 372, pp 631, 1994. Sander, Holm et al also did  
> some nice work along these lines.
> 
> Andrej
> 
> P.S. My own hard number related to this argument is that about one third  
> of currently deposited PDB structures have significant sequence similarity  
> to at least one already deposited PDB structure (>30%).

This of course assumes that the currently determined PDB structures
are a random selection of protein sequences, which I think is 
unlikely, but someone can correct me if he/she has evidence.

(I have no idea either how robust this sort of extrapolation would be
either as you started to deviate from a Normal distribution....)

ewan




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