From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Apr 30 2010 - 12:08:48 CDT
Google also reveals http://www.sbg.bio.ic.ac.uk/~maxcluster/.
If you are only interested in parts of the structure you could calculate the
RMSD between those parts and use that as the distance metric in any number
of generic clustering algorithms (for example R <http://www.r-project.org/>or
Bioshell <http://bioshell.chem.uw.edu.pl/clust.html>).
Regards,
Ajasja
On Fri, Apr 30, 2010 at 11:40, Nicholas M Glykos <glykos_at_mbg.duth.gr> wrote:
>
>
> > I would like to cluster different conformations of a protein focusing on
> > certain residues and their side chains. Is there any available
> > softwares/algorithms that would perform this?
>
>
> If you assign to the atoms you are interested-in a distinct SEGID,
> say L, then you can use
>
> # carma -v -w -col -cov -eigen -dpca 5 3 298 -segid L protein.dcd
> protein.psf
>
> for performing a PCA-based clustering in dihedral space (which ignores
> side chains), or better,
>
> # carma -v -w -col -cov -eigen -proj 5 3 298 -segid L -atmid HEAVY
> protein.dcd protein.psf
>
> for performing a PCA-based clustering (using all heavy atoms) in Cartesian
> space. If you'd rather be safe than sorry, you can use something like
>
> # crossDCD protein.psf protein.dcd protein.dcd 200 " -segid L -atmid HEAVY
> "
>
> to prepare a square matrix with all frame-to-frame rmsds between the
> selected atoms (all heavy atoms of SEGID L) which you can then use with a
> statistics program (like R) for cluster analysis. Both carma and
> the crossDCD script are available from
> http://utopia.duth.gr/~glykos/Carma.html
>
>
> Nicholas
>
>
>
> --
>
>
> Dr Nicholas M. Glykos, Department of Molecular Biology
> and Genetics, Democritus University of Thrace, University Campus,
> Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
> Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
>
>
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