[BioPython] Structural alignment

[Andrew Dalke]

Iddo Friedberg wrote:
> 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

Though it's perhaps a bit easier problem since the original poster,
Omid, wants
>> 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.

If it's two conformations of the same structure and the goal is
to minimize overall RMSD through a single global alignment matrix
then the usual reference I know is Kabsch

[Kabsch, 1976] Kabsch, W. (1976). A solution for the best rotation
    to relate two sets of vectors. Acta. Crystal, 32A:922-923.
[Kabsch, 1978] Kabsch, W. (1978). A discussion of the solution
   for the best rotation to related two sets of vectors. Acta. Crystal,  
34A:827-828.

(The first had an ambiguity that could cause a sign error; fixed
in the second.)

Several structure program implement that including:
   O - http://xray.bmc.uu.se/usf/factory_4.html
   VMD - http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node183.html
   PyMol - http://www.pymolwiki.org/index.php/Kabsch

This algorithm is not mentioned on the Wiki page and is 11 years older
than the oldest mentioned reference.  It isn't NP-hard
as alluded to in the Wiki, since it's solving a much simpler problem.

The date for ProFit is strange on the Wiki.  I knew about ProFit before
the claimed 1996. The web site says
  http://www.bioinf.org.uk/software/profit/faq.html

> No paper has been published describing ProFit itself since it is  
> simply a convenient program (I hope) to let you use a standard fitting  
> algorithm; consequently, it is a little difficult to reference. The  
> exact wording is up to you and dependent on the context, but I suggest  
> something similar to:
>
> Fitting was performed using the McLachlan algorithm (McLachlan, A.D.,  
> 1982 ``Rapid Comparison of Protein Structres'', Acta Cryst A38,  
> 871-873) as implemented in the program ProFit (Martin, A.C.R.,  
> http://www.bioinf.org.uk/software/profit/).

The McLachlan algorithm is also not mentioned in the Wiki.

I found a usenet announcement about ProFit at
http://groups.google.com/group/bionet.software/msg/f219c5163bbadbdc? 
dmode=source&hl=en

> From: mar... at bsm.bioc.ucl.ac.uk (Andrew Martin)
> Subject: ANNOUNCE: Protein Fitting Software
> Date: 1995/07/20
> Message-ID: <1995Jul20.101545.37119 at ucl.ac.uk>#1/1
> X-Deja-AN: 106640715
> organization: University College London
> newsgroups: bionet.software
>
> I've finally (after about 2 years) got around to fixing the last (?)
> remaining bugs in my ProFit protein least-squares fitting software and
> decided to make it generally available.

so the date should be 1995 or 1993 or earlier.  I suspect the 1996
date came from the "first written" date for the documentation, at
   http://www.bioinf.org.uk/software/profit/doc/

Well, that was entirely too much information about a minor nit!
I cc'ed as it were this email to the wiki page, but I don't like
learning wiki formatting rules so put it on the talk page.

					Andrew
					dalke at dalkescientific.com