Subject: NCI SMILES Database

From: "M. Nicklaus" <[email-masked]>
Date: Tue, 9 Sep 1997 19:12:17 -0400 (EDT)

The promised SMILES version of the open part of the NCI database is
up on http://epnws1.ncifcrf.gov:2345/dis3d/3ddatabase/nci_smil.html
and ready for download.  (Thanks to Dan Zaharevitz for his help with
this.)

In fact, two versions of the SMILES database are available.  Thanks
to Wolf-Dietrich Ihlenfeldt, we re-converted the NCI database with
the program CACTVS v. 3.2, using conversion scripts provided by Wolf-
Dietrich that handle formal charge problems and took care of other 
'weird stuff' in the NCI database.  

The other conversion program used is Babel, v. 1.6.  The formal charge 
problem regarding nitro groups was fixed by simple string substitution 
in the Babel output; none of the other potential problems was addressed.  

We found that the output of the two programs differ substantially if one
just does a simple string comparison.  For the first 1000 NSC numbers, 
64% of the SMILES strings showed differences between Babel and CACTVS. 
This does not mean, however, that either one of the differing SMILES
strings for the same compound need be wrong, since neither conversion
program claims to generate Unique SMILES (to our knowledge).

For this reason, we decided to make both versions available.  If you 
compare them to each other, we'd be interested to know which one you 
find better, more correct, more useful for a certain purpose etc.  
No further evaluation was conducted on either database, so please 
PERFORM YOUR OWN CHECKS before you use the SMILES strings for any given
purpose.

Both versions contain SMILES strings for the same set of 237,771
structures.  The files are just over 4 MB compressed, and uncompress
to about 15 MB each.

Marc C. Nicklaus & Bruno Bienfait

------------------------------------------------------------------------
 Marc C. Nicklaus, Ph.D.                 National Institutes of Health
 E-mail: [email-masked]               Bldg 37, Rm 5B29
 Phone:  (301) 402-3111                  BETHESDA, MD 20892-4255    USA
 Fax:    (301) 496-5839    http://www.nci.nih.gov/intra/lmch/MCNBIO.HTM
    Laboratory of Medicinal Chemistry, National Cancer Institute,  &
  Lab. of Structural Biology, Div. of Computer Research and Technology
------------------------------------------------------------------------