[BioC] calculate interaction between aminoacids residues

[w.huber at dkfz-heidelberg.de]

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.

  Best wishes
    Wolfgang

-------------------------------------
Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax:   +49 6221 42524709
Http:  www.dkfz.de/abt0840/whuber
-------------------------------------

> Fabien Crozet <fabien_crozet at yahoo.fr> writes:
>
> >>From a particular PDB file I would like to calculate
> > the interactions between residues. Two residues are
> > considered interacting if any of their atoms
> > (excluding hydrogen) are within a particular cutoff
> > distance.
> > The main goal is to compare 2 PDB files with little
> > differences and then determines the number of
> > interactions that are disrupted.
> > I wonder if there are bioconductor package that can be
> > adapted for these kinds of statiscal analysis... I
> > don't know too much about the differents packages and
> > if someone can give me a suggestion for it, i would
> > appreciate a lot !
> > Thanks for help.
> >
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>
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