correlated mutations

[Ewan Birney]

Aare Abroi wrote:
> 
> Hallo !
> 
> I have a question about correlated mutations. For example is it possible to
> find amino-acids which are involved in receptor-ligand interaction by
> analyzing receptor and ligand protein families  (I mean the some receptor or
> ligand sequences from different organisms). The complementary surfaces may
> by mirrored in correlated mutations in sequences. If there are some programs
> which do this work could you please let me know.
> 
> --
>        Aare Abroi                 Estonian Biocentre
>      aabroi at ebc.ee                    Riia 23
>   tel. +372 7 420 223              Tartu, EE2400
>   fax: +372 7 420 286                 Estonia

This questions is actually harder than it looks as it relies 
implicitly on understanding the evolution of the proteins 
involved  - ie you have to have a good tree at first. 

some time ago I tried to write a program that would look for
correlation inside a single alignment. This would be identical
to the receptor ligand problem as one could concatonate the alignments
of the two proteins as one...

but the program didn't work at all well (well -- I wrote it a long
time ago). If anyone has a good algorithm for tackling this problem
I'd love to hear about it


ewan


birney at molbiol.ox.ac.uk
http://www.ocms.ox.ac.uk/~birney/me.html