[BioC] calculate interaction between aminoacids residues

[Aedin Culhane]

In addition to those programs mentioned by Fabien, I think that Willie
Taylor's program SAP should calculate the RMSD (root mean square deviation)
between all pairs. Also SwissPDB viewer is very nice for visualising
distance between two or multiple protein sequences.  In SwissPDB viewer the
amino acids in a protein structure can be coloured by distance to another
protein.  This visualisation can be very useful if you are generating
protein models (and for presentations).

Aedin




-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Junwen wang
Sent: 29 October 2003 13:28
To: Fabien Crozet
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] calculate interaction between aminoacids residues


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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