Looking for molecular-similarity soft and 3D databases.

Pedro M Coutinho pedro at iastate.edu
Wed May 24 15:21:51 EST 1995

In article <3pvh8b$rgj at mserv1.dl.ac.uk>, <angstrom at medvax.sunet.se> writes:

|> I'm looking for a software and a 3D-database to do molecular-similarity 
|> searches. What I am trying to do is to "mimic" certain possible epitopes on 
|> carbohydrates using other small, non-carbohydrate molecules.
|> Does anybody know about such a program and/or available 3D-databases of 
|> small molecules? Are there any available in Internet?

|> Ernesto Moreno


You can find the NCIOPEN database of automatically generated 3-D structures in
the URL <ftp://helix.nih.gov/ncidata/3D/>. A copy of the readme file
found there is given below. A single file containing 126089 3D-structures in 
MDL format (only heavy atoms) can be found there.

Files can be converted to many other formats (and hydrogen atoms added) using 
babel <http://mercury.aichem.arizona.edu/babel.html>. 

Concerning software you probably should give a look at DOCK found in the URL

Please post other suggestions that you might have received!


Pedro Coutinho

--------------------------------- H2N-CH-CO-NH-CH-CO-...-NH-CH-COOH --
Pedro M. Coutinho  - Graduate Student  \        \            \        
IOWA STATE UNIVERSITY                   R1       R2           Rn      
Department of Chemical Engineering               Phone: 1-515-294-9370
2114 Sweeney Hall                                Fax:   1-515-294-2689
Ames, IA 50011-2230                          E-mail: pedro at iastate.edu
U.S.A.                      URL: http://www.public.iastate.edu/~pedro/

--------------- Copy of nciopen3d.readme -----------------------------

File: nciopen3d.mol.Z (compressed with the UNIX command compress)

The structures in this file are the compounds of the open open part of 
the NCI database (nciopen.mol) plus the 3D-atomic coordinates as an MDL 

The compressed file takes about 34 MByte, the uncompressed file about 
180 MByte.

The coordinates were generated by the 3D-structure generation program 
Corina. Lacking stereodescriptors were added by the program in order to 
fulfil simple geometric requirements, i.e., there is no guarantee for 
finding the stereoisomer with lowest energy.

Statistics of the Corina run:

   Corina version 1.5 (December 1994)

   Platform: Silicon Graphics Indigo 2 running IRIX 5.2

   CPU time: 33650 sec - 0.27 sec/mol

   Structures read: 
      126705 compounds - 100.0%

   Structures converted:
      126089 compounds -  99.5%

   Structures excluded due to atoms having more than six neighbors:
         327 compounds -   0.3%

   Structures not converted due to internal problems:
         289 compounds -   0.2%
References on Corina:
   (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.


   Prof. Dr. Johann Gasteiger and Dr. Jens Sadowski
   Universitaet Erlangen-Nuernberg
   Naegelsbachstrasse 25
   D-91051 Erlangen

   email: Gasteiger at EROS.CCC.Uni-Erlangen.DE
          Sadowski at EROS.CCC.Uni-Erlangen.DE

   FAX: +499131/85-6566

Pedro M Coutinho
pedro at iastate.edu

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