Subject: Looking for info on alignment/superposition

From: [email-masked] (Joe M Leonard)
Date: Wed, 5 Jan 1994 00:48:55 -0500

Folks,
	I'm interested in learning of programs that perform superposition of
 chemical structures in several ways:

1. Generalized field-fitting (steric and property grid), with no consideration
of the molecular connectivity.  An example of this would be a program to
align f(mol2) with f(mol1), while varying the 3D rotation translation matrix
of mol2.

2. Superposition involving the connectivity, but permitting alignment of a 
(sub)set with another (sub)set.  An example of this would be a program to 
align mol2 with mol1, based on a explicit or implicit list of atom pair/group
relationships.

3. Superposition assuming identical connectivities.  An example of this
would be a program which measures the RMS difference between
individual structures obtained from a conformational analysis.

As I see it, the difficulty and computational cost increases (3) -> (2) -> 
(1).  All of these approaches can be made "more interesting" by considering
mol2 to be (a) flexible or (b) a list of structures.  I also remember
comments that suggest this is an active area of research (even though I
can't find much in the small number of journals I have easy access to).
I'm interested in hearing of individual programs, or references/pointers to
the appropriate literature.  

Naturally, I'll summarize for the net.  Thanks in advance!

Joe Leonard
[email-masked]