[BioC] calculate interaction between aminoacids residues

Junwen wang junwen at astro.ocis.temple.edu
Wed Oct 29 14:27:46 MET 2003

You may use some software that can superimpose two PDB files, such as
MAMMOTH, VEST or DALI. The programs will provide the  coordinates and you
can then calculate their distances. But most of the programs only
superimpose a-carbon of the residue.

Good luck!

On Wed, 29 Oct 2003, [iso-8859-1] Fabien Crozet wrote:

> >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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