[BioC] calculate interaction between aminoacids residues

[A.J. Rossini]

w.huber at dkfz-heidelberg.de writes:

> Hi,
>
>> As far as I'm aware, we don't yet have code to compute with proteins,
>> though that is something that would be useful to do.
>
> but R has lots of facilities for matrix and vector calculation. As far as
> I understand, a protein in the sense of PDB is just an n x 3 matrix of
> coordinates, with the n the number of atoms. (Plus factors of length n
> with the atomic element, residue ID...). To do what Fabien has in mind,
> he would simply calculate the pairwise distances between all atoms in
> protein1 versus all atoms in protein2, and then look at the distance
> matrix.

I definitely agree, but I'm thinking about the difference between
computing with proteins and computing statistics -- we could do much
of what we are doing now with R without Bioconductor, but it's far
less intuitive and provides less of a macro view of the world and less
of a straightforward view of the operations that one wants to do on
the data.

best,
-tony
-- 
rossini at u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
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