Subject: RMS Fits For Structures That Have Symmetry

From: [email-masked] (Dr. Golender Valery)
Date: Thu, 11 May 1995 14:44:20 +0300

Jim Given recently asked about calculation of 'RMS Fits For 
Structures That Have Symmetries'. It fact the same question was 
discussed on CCL in February when Dongchul Lim asked how one 
can tell if two conformers are the same. But I see from postings of 
Gregory Nikiforovich (Hi!) and Graham Hurst  that discussion is open 
again. I already mentioned then that we developed a conformer 
clustering algorithm that takes into account molecular symmetry. This 
algorithm generates chemical graph automorphisms (atom mappings 
that preserve chemical structure) using an efficient algorithm based on 
graph potential method. This method generates very sensitive graph 
invariants that allow significantly reduce the number of possible 
permutations from the worst case of N! (as mentioned by Graham 
Hurst). For the graph potential method description see paper
Golender V.E., Drboglav V.V., Rosenblit A.B. Graph potentials 
method and its applications for  chemical information processing. 
J.Chem. Inform. Comput. Sci., 1981, v.21., No.4, 196-204
and book
Golender V.E, Rozenblit A.B. Logical and Combinatorial Algorithms 
for Drug Design. Research Studies Press: UK (1983).
Conformer clustering algorithm that incorporates checking of 
molecular symmetry is a part of Apex-3D system for drug design 
marketed by Biosym Technologies. The algorithm allows also 
selection of  atoms only from "important" groups, as Gregory 
Nikiforovich wants to see.

After my previous posting I got a number of requests for additional 
information about the algorithm. In order to make the information 
publicly available I will put it on WWW:

http://www.dcl.co.il/conf_clust.html

I will be able also to provide additional information on request.

Sincerely,

Valery Golender, Ph.D.
Director, Chemical Software
DCL Systems International Ltd
20 Galgalei Haplada St. POB 544
Herzlia 46105 ISRAEL
Tel: + 972-9-584-684
Fax: + 972-9-543-917
E-mail: [email-masked], [email-masked]