[Biopython] clustering pdb

[Christian Schaefer]

On 07/19/2010 11:39 AM, Bala subramanian wrote:
> Friends,
> I have around 3000 pdb files obtained from MD simulations. I would like to
> know if it is possible to cluster the pdb files using any of the biopython's
> bio.PDB or other modules. If so, i would appreciate if you could provide me
> a sample code.

It depends on what you mean by 'clustering'. If you refer to sequence 
clustering, i.e. redundancy reduction on sequence level, there are 
several tools out there (like CDHit) for that purpose. Not sure if 
there's a native implementation in BioPython for that.

Chris

-- 
Dipl.-Bioinf. Christian Schaefer
Technical University Munich
Department for Bioinformatics
Faculty of Computer Science/I12
Boltzmannstr. 3
D-85748 Garching b. Muenchen
Germany
http://www.rostlab.org/~schaefer