Subject: Superimpose/Superposition cyclic peptides

From: [email-masked]
Date: Wed, 15 Aug 2001 19:53:11 +0200

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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