Subject: Re: CCL:Looking for RMS distance calculator

From: "Peter Shenkin" <[email-masked]>
Date: Tue, 12 Apr 1994 15:02:03 -0400

On Apr 11, 12:56pm, Luca Jovine wrote:
> Subject: CCL:Looking for RMS distance calculator
>
> Dear Netters,
>
> I am looking for a program that could calculate a RMS distance matrix
> for a set of homologous molecular structures (possibly in PDB format).
> It would be even better if such program allowed to pick which parts of
> the structures to compare....

Our program, XCluster, does this as a first step in performing cluster
analysis;  however, the molecules it takes have to be very highly homologous
indeed: they have to be conformers.  Extension to a mixed ensemble with a
common substructure is something we want to do, but it's not there now.

If what you are looking at is homologous proteins, please see Holm and Sander,
JMB, 233, p123 (1993).  Their similarity measure between two proteins is not
the
rigid-body RMS, but rather the RMS of corresponding elements of the two
internal
alpha-carbon distance matrices (or something very close to that).  They do have
provision for performing frame-shifts and deletions for better aligning the two
chains prior to final assignment of the "distance" between the two.

XCluster is bundled with the MacroModel modeling package;  for more info,
try "finger [email-masked]", or send me email.  We have a
paper in press with J. Comput. Chem.

>    "I'll give you a definitive maybe" (Sam Goldwyn)

I suppose this is what I said;  but at least I didn't say, "In two words: im
possible." (also attributed to Sam)   :-)

	-P.

-- 
********************** "So much for global warming...." *********************
Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ.,
New York, NY  10027;     [email-masked];     (212) 854-5143
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