Subject: Re: CCL:Superimpose/Superposition cyclic peptides

From: Peter Shenkin <[email-masked]>
Date: Thu, 23 Aug 2001 09:45:55 -0400 (EDT)

Hi,

XCluster, which is part of the MacroModel package, can come close,
provided the backbone atoms you wish to superimpose are actually
cyclic.

For instance, suppose you were superimposing just CA's of a
pentapeptide and the CA's have atom numbers 1, 4, 7, 10, 13.
The program (if told to observe cyclic symmetry), would compare
each pair of conformations 10 ways, picking the lowest RMS as
the value it would use in the clustering.

If conf 1 has the atoms in the above order, conf 2 would be
compared in the following registrations with conf 1:

	1  4  7  10  13
	4  7 10  13   1
        1 10 13   1   4
        ... (2 more like this)
        1  13 10   7   4
        13 10  7   4   1
        10  7  4   1  13
        ... (2 more like this)

The problem is that you probably don't want the second 5 ways.

The next version of the program (due out in Oct or Nov of this
year) will have automatic symmetry detection, and would do all
this automatically, including keeping just the comparisons
consistent with the overall symmetry of the system.

Obviously, you do want to compare things in both directions
if the ring atoms look the same going around in both directions,
as in cyclohexane.

You can learn more about how it's done now by going to our
web site, then support, then on-line manuals, then XCluster.

Hope this helps,
-P.

On Wed, 15 Aug 2001 [email-masked] wrote:

> Dear CCL'ers,
>
> starting a new project on the conformational properties cyclic penta-
> and hexapeptides the following problem came up:
> I have about 50 different cyclopeptides with a known 3-dimensional conformation
> (either determined by experiments or obtained by strucutural calculation using
> molecular dynamics). My goal is to take these structures, cluster their backbone
> conformations and derive some conformational families.
> Unfortunately, the residue numbering within the cyclic peptides is somehow
> arbitary, thus preventing a simple atom-on-atom superimposing, e.g. the molecule
> cyclo-(Pro-Ala-Ala-Ala-Ala) could have the same conformation as cyclo-(Ala-Ala-
> Pro-Ala-Ala) but it is not detected by common superimposing fomralisms, because
> the numbering scheme of the residues is different (the Pro's have the number 1
> and 3 respectively).
> Does anyone knows about a programm or formalism which could help me to tackle
> this problem? Any hint is appreciated and will be posted on CCL.
>
> Thanx in advance,
> Robert
>
> +---------------------------------------------------------------+
> | Dr. Robert Guenther     [e-mail:Robert.Guenther(at)ch.tum.de] |-+
> | Institut fuer organische Chemie und Biochemie II, TU Muenchen |#|
> | Lichtenbergstr. 4, D-85747 Garching                           |#|
> +---------------------------------------------------------------+#|
>  +----------------------------------------------------------------+
>
>
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-- 
  Peter S. Shenkin                      Schrodinger, Inc.
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