Subject: Summary: Algorithm to build 3D molecule

From: Yongxing Liu <[email-masked]>
Date: Tue, 04 Nov 1997 16:32:13 -0500

Dear CCLers, 

Thanks for all who answered my questions. 

********************* The  Original Question ****************

 I am looking for algorithms to build 3D coordinates of small  molecules for
further refinement. The inputs are atomic element
type(H,C,N,O,etc),connectivity and bond order only. The output will be the
3D coordinates for each atom.

**** Answer From Professor Richard Gillilan ************

   I see that the NCI database was built from connectivity files
using Chem-X. There is a useful discussion about the limitations
and failures of the method on 

http://epnws1.ncifcrf.gov:2345/dis3d/3Ddatabase/chemx/tech.html#build

The page also gives a pointer to the CONCORD software (TRIPOS).

The readme file that came with the version of the NCI database
I downloaded a year ago talks about the Corina program:

  (1) Sadowski, J.; Gasteiger, J. "From Atoms and Bonds to Three-
       Dimensional Molecular Models: Automatic Model Builders."
       Chem. Rev. 1993, 93, 2567-2581.

   (2) Sadowski, J.; Gasteiger, J.; Klebe, G. "Comparison of Automatic
       Three-Dimensional Model Builders Using 639 X-Ray Structures."
       J. Chem. Inf. Comput. Sci. 1994, 34, 1000-1008.

****** Answer from Dr. Zhaowen Luo *********

As far as I know, CONCORD is a popurlar algorithsm for that. It is
commerical available. Following is the description:

      CONCORD is a program developed at the University of Texas at 
      Austin for the rapid generation of high quality approximate
      3-dimensional molecular structures. 

I think CONCORD is a doctoral thesis.

*****  Answer form Dr. Wang Arthur *****

The problem that you have encounted is called 2D to 3D conversion. No 
doubt many successful algorithms have been developed, such as CONCORD, 
CORINA, CONVERTER ... 

**** Many other people pointed me to their programs, Thanks too. ****

Yongxing Liu
Department of Chemistry
Wesleyan University
Middletown CT 06459

E-mail [email-masked]
Telephone: 860-685-2777
Fax:       860-685-2211
Http://linus.chem.wesleyan.edu/yliu/