Subject: summary: Superpose algorithm

From: Fenglou Mao <[email-masked]>
Date: Fri, 12 May 2000 09:13:23 +0800 (CST)

>From Nick Jewell,

If I've got this right, some superposition algorithms (for small
molecules)
include:

Flex-S : http://www.tripos.com by Gerhard Klebe
ASP: http://www.oxmol.co.uk by Kate Burt and Graham Richards
FBSS: http://cisrg.shef.ac.uk by Dave Wild and Peter Willett

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>From Anselm Horn,

try the quatfit program in the CCL archives (references are given within).

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>From Jarrod Smith,

Kearsley, Simon K; "An Algorithm for the Simultaneous Superposition of a
Structural Series"; J. Comp. Chem., 11, 1187-1192 (1990).

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Found by myself,

Ferro D R and J Hermans 1977, A Different Best Rigid-body Molecular Fit
Routine, Acta Crystallography A33:345-347

Kabsch W 1978. A Disscussion of the Solution for the Best Rotation to
Relate Two Sets of Vectors. Acta Crystallography A34:827-828.

Sincerely Yours,

FengLou Mao
*******************************
ADD:Mr. FengLou Mao
    Institute of Physical Chemistry
    Peking University
    BeiJing
    P.R.China
Tel:86-10-62756833
Fax:86-10-62751725

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From: James Smith <[email-masked]>
Date: Fri, 12 May 2000 11:42:09 +0100 (BST)

We use: 

Gerber & Muller (1987) Superimposing Several Sets of Atomic Coordinates,
Acta Cryst, A43, 426-428

Perkins & Dean (1993) An exploration of a novel strategy for superposing
several flexible molecules, J. Computer-Aided Molecular Design, 7, 155-172

Also  McLaughlin's algorithm  for superposing two molecules. Which also
allows the use of null correspondances

Could have a look at:

 Masek, Merchant and Matthew's method also uses Molecular Skins: A New
Concept for Quantitative Shape Matching of a Protein with it Small
Molecule Mimics

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