[BioPython] Structural alignment

[Iddo Friedberg]

I think your question is better directed to the pdb-l list.

pdb-l at sdsc.edu

The unlike sequence alignemnt, structure alignment is not such a
well-defined quesiton, and the answer you get depends a lot on your
prerequisites.

There are quite a few publically available structure alignment programs.
Surprisingly, Wikipedia has a nice list. (OK, I wrote in a few of the
table entries. Guilty!).

http://en.wikipedia.org/wiki/Structural_alignment

Cheers,


Iddo


--
Iddo Friedberg, Ph.D.
Burnham Institute for Medical Research
10901 N. Torrey Pines Rd.
La Jolla, CA 92037, USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171
http://ffas.ljcrf.edu/~iddo

On Mon, 14 Nov 2005, Omid Khalouei wrote:

> Hello,
> 
> I was wondering what's the current common practice to align two different 
> structures belong to the same protein. In particular I want to align two 
> HIV-1 protease structures obtained from PDB and get the RMSD. I know how to 
> do this with Swiss-PdbViewer, using the "majic fit". In a paper they have 
> done this with the program MOLMOL but I am having difficulty installing it 
> on my Windows computer since the program is meant to be used by Linux/Unix 
> machines.
> Are there any other efficient publicly available tools for this purpose?
> 
> Thanks for your help,
> Omid K.
> 
> 
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