Subject: Summary- 3-D Structure File

From: "Craig Shelley" <[email-masked]>
Date: 30 Oct 1995 14:09:31 -0700

Reply to:   Summary: 3-D Structure Files

A couple weeks ago, I posted to the CCL inquiring about free or public domain
databases of 3-D structures.  The following are my responses.

Craig Shelley
[email-masked]

_________________________________________________________
From: Abby Parrill (10/13/95)

One source of public domain 3D structural coordinates is the Brookhaven 
Protein Data Bank (for proteins and some biological molecules which are 
targeted by proteins, there are some DNA sequences and the like also).  
Anonymous ftp to pdb.pdb.bnl.gov.

                      Abby Parrill
                  Chemistry Department
      Artificial Intelligence in Chemistry Laboratory                         
                The University of Arizona                    
             [email-masked]              
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From: Toni Kazic (10/12/95)

Klotho has 439 structures with pseudo-energy-minimized 3D coordinates.
They are headed for the public domain, but in the meantime you can get to
them from http://ibc.wustl.edu/klotho/.  All are metabolites.
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From: Rzepa,Henry (10/13/95)

One with small molecules is
http://ws05.pc.chemie.th-darmstadt.de/vrml/pdbvis.html

Dr Henry Rzepa,  Department of Chemistry,  Imperial College,  LONDON SW7 2AY;
[email-masked] via Eudora Pro 2.1.3; Tel  (44) 171 594 5774; Fax: (44) 171
594 5804.
World-Wide Web URL: http://www.ch.ic.ac.uk/rzepa/  
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From: Dr. Jens Sadowski              (10/13/95)
------------------------------------------------------------
| Dr. Jens Sadowski            Tel.: +49 (0)202-364674     |
| Bayer AG                     Fax:  +49 (0)202-368552     |
| PH-R Structural Research     Email: [email-masked] |
| Aprather Weg                                             |
| D-42096 Wuppertal, Germany                               |
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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).

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
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From: Dr. Dave Winkler (10/12/95)

I have the NCI cancer database (~100K structures) and the Maybridge catalog
database (~40K structures). Also Garland Marshall at Washington University,
St Louis has a program DBMAKER which can generate large 3D databases,
either randomly, or based on a specific structural core.

Dr. David A. Winkler                            Voice: 61-3-542-2244
Principal Research Scientist                    Fax:   61-3-543-8160
CSIRO Division of Chemicals and Polymers        CSIRO: http://www.csiro.au
Private Bag 10,Rosebank MDC, Clayton, Australia       http://www.chem.csiro.au
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