proteins with 30% homology should have the same general fold: reference for this ?
Gerald.Loeffler at vienna.at
Tue Jul 21 03:25:38 EST 1998
I've not followed this thread, but just in case nobody came up with this
The paper I normally associate with the relationship of sequence
identity and structural similarity is
Sander, C. and Schneider, R. (1991)
Database of homology-derived structures and the structurally meaning of
Proteins, 9, 56-68.
I'm not sure whether this is the first published work that directly
examined this aspect of sequence-structure relationship, though. And I'm
sure there were many afterwards...
Scott Le Grand wrote:
> My failing memory indicates this observation was first made by Cyrus Chothia in the
> 1970s or so after a lot of empirical comparison along the lines that Ram suggests.
> appears to be one of the rules of thumb that falls out of the process of protein
> rather than some sort of natural law as the aforementioned Paracelsus challenge
> illustrated in short order. Of course, the Paracelsus challenge begs the question
> of just how close naturally evolved proteins out there can get and possess truly
> Scott Le Grand
> VM Labs
> Dr. Ram Samudrala wrote:
> > Eric Campeau <ecampe at po-box.mcgill.ca> wrote:
> > > every teacher in protein structure classes say that if a protein has a 30%
> > >homology to a related protein, it should have the same general fold. However,
> > >they do do not cite the reference to this .... is there anybody that could give
> > >me the reference for this "fact" ?
> > Well, you can just do a few sequence comparisons for proteins with
> > known structure and see if the folds are the same. So it's completely
> > testable. Though I'd add that this "rule" applies only to proteins in
> > nature and not to designed proteins (cf. the Parcelus challenge).
> > --Ram
> > email at urls || http://www.ram.org || http://www.twisted-helices.com/th
> > The dollar will never fall as low as what
> > some people will do to get it.
> > ---Alfred E. Neuman
Gerald Loeffler - Bioinformatics Scientist
Boehringer Ingelheim R&D Vienna, Molecular Biology Department
Email: Gerald.Loeffler at vienna.at
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