modelling protein structPRINTures

Andrej Sali sali at tamika.rockefeller.edu
Sat Jan 28 14:08:42 EST 1995


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
> 
> 
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> 

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%).




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