sequence alignment poorer than 3D alignment

Simon Brocklehurst simon.brocklehurst at camb-antibody.co.uk
Thu Sep 17 06:37:21 EST 1998


Michel PETITJEAN wrote:

> Is there some pair of proteins having a sequence homology (% similarity)
> significantly lower than their % 3D-similarity ? (any definition of
> these percentages should work). References are welcome. Thanks.

Michel,

There are many examples of what you're looking for.  For example, have a
look at the collection of 3-D structure-based alignments, and corresponding
pairwise sequence identity matrices on the Web server in Tom Blundell's
group in Cambridge:

http://merlin.bioc.cam.ac.uk/~campass/superfamily.html

Depending on your requirements, you may wish to focus on a lesser number of
cases where there is no detectable level of similarity at all at the
sequence level (e.g. no conservered hydrophobic residues). These can be
identified by 3-D structure superpositions, and predicted by methods which
take into account correlated amino acid residue substitutions (e.g.
threading).

Regards,
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.catplc.co.uk/
mailto:simon.brocklehurst at camb-antibody.co.uk




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