[BioC] calculate interaction between aminoacids residues

[Junwen wang]

On Wed, 29 Oct 2003 w.huber at dkfz-heidelberg.de wrote:
> 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.
You need to take care of two more things as I can think of;
1. if the two proteins have long helix, the algorithm will focus on
the helices and get low RMSD (Residue mean score distance). But other
parts are aligned urgly, the alignment will not be good in a biologist's
view.
2. there are some residues that are not alignable(they are two far apart).
These residues should not be taken into account when calculating the
final RMSD.

Regards
Junwen
>
>   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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> >
> > --
> > 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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