[Biopython] clustering pdb

[João Rodrigues]

Hey,

You can try this:
http://sbcb.bioch.ox.ac.uk/oliver/software/GromacsWrapper/html/edpdb.html

Best!

João [...] Rodrigues
@ http://doeidoei.wordpress.org



On Mon, Jul 19, 2010 at 12:07 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Mon, Jul 19, 2010 at 10:59 AM, Bala subramanian
> <bala.biophysics at gmail.com> wrote:
> > Hello peter,
> > Sorry for the incomplete information. I want to cluster the structures
> say
> > for example using rmsd between the pdb.
> >
> > Thanks,
> > Bala
>
> Provided you can specify the atomic mapping between the structures,
> you can calculate RMSD using Bio.PDB, see for example:
> http://www.warwick.ac.uk/go/peter_cock/python/protein_superposition/
> One way to do this would be pairwise sequence alignments. There
> are probably specialised tools out there for this sort of clustering...
>
> Peter
>
> P.S. Please try to CC the mailing list in replies.
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