Subject: NCI 3D Database

From: [email-masked]
Date: Fri, 3 Mar 1995 08:41:31 +0100

The open NCI database is now available with Corina-generated
3D-coordinates.

Recently, NCI made the 125,000 connection tables of the open part of
the NCI structural database freely available. We have built 3D-models
>from the connection tables using our 3D-structure generator Corina.

NCI kindly allowed us to make these data available from the same server
where the original database can be downloaded from.

The file is available as an MDL SDFile via anonymous ftp:

   ftp helix.nih.gov.
   login: anonymous
   password: <your email address here>

   cd ncidata/3D

In this directory are two files: an nciopen3d.readme file and the UNIX
compressed data file nciopen3d.mol.Z (~34 MByte).

I enclose a short description of the 3D-generation procedure.

If you have any questions or problems please contact me.

Jens Sadowski

------------------------------------------------------------------------------
| Dr. Jens Sadowski                                                          |
|                                                                            |
| Computer-Chemie-Centrum           Tel.: +49 (0)9131 85-6569                |
| Universitaet Erlangen-Nuernberg   FAX:  +49 (0)9131 85-6566                |
| Naegelsbachstrasse 25             Email: [email-masked] |
| D-91052 Erlangen, Germany                                                  |
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--- Begin included message ---------------------------------------------------

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.

Information:
 
   Prof. Dr. Johann Gasteiger and Dr. Jens Sadowski
   Computer-Chemie-Centrum
   Universitaet Erlangen-Nuernberg
   Naegelsbachstrasse 25
   D-91052 Erlangen
   Germany
 
   email: [email-masked]
          [email-masked]
 
   FAX: +49 9131/85-6566