[BioPython] Structural alignment

[Omid Khalouei]

Thanks alot, the wikipedia site links are indeed a good collection put 
together. It's interesting that sometimes what you get from these sites is 
more informative than hours of searching on scientific search engines. I 
also realized that it's better if I use the keywords structural 
"superposition" rather than "alignment" for my purpose.

Thanks again,
Omid K.


>From: Iddo Friedberg <idoerg at burnham.org>
>To: Omid Khalouei <omid9dr18 at hotmail.com>
>CC: biopython at biopython.org
>Subject: Re: [BioPython] Structural alignment
>Date: Sun, 13 Nov 2005 22:41:01 -0800
>
>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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>