Subject: CCL: Announcement: New web service for chemical databases - beta testers sought

From: "M. Nicklaus" <mn1~at~helix.nih.gov>
Date: Thu, 9 Sep 2004 18:09:19 -0400 (Eastern Daylight Time)

We are about to go online with a beta version of our new web service that
makes publicly available several databases from both U.S. Government
sources and commercial sample suppliers. Both bulk files and web-based
search interfaces similar to the one of the current Enhanced NCI Database
Browser (http://cactus.nci.nih.gov/ncidb2/) are, or will soon be made,
available.

We are looking for people who are interested in being beta testers.

We have currently about 20 different databases, ranging from very small
data sets (<10 compounds) to databases with >400,000 compounds.  The
current total is about 1.8 million compounds, with about 650,000 coming
> from public U.S. Government databases, and 1,150,000 from screening sample
catalogs from suppliers who agreed to let us re-post their databases.  We
gratefully acknowledge their contributions to our new site.

We are also introducing a new set of identifiers, included for each of the
compounds in the above data sets. They are based on CACTVS hash codes, and
were developed in close collaboration with Wolf-Dietrich Ihlenfeldt, the
author of CACTVS.

One of these identifiers is a hash code that is tautomer-invariant but
sensitive to most everything else that distinguishes compounds, such as
stereochemistry, isotopes, counter ions etc.  We think that this
*calculable* identifier (dubbed the "FICuS" ID by us) comes closest to
distinguishing between chemicals, i.e. the "stuff in the bottle," the way
a chemist would do it.  We have found this identifier a powerful tool in
our analyses for very rapidly identifying if a chemical is already in
one's collection, for determining the intra-database duplication rate and
inter-database overlap, for merging databases etc.  A special index file
format allows one to perform these operations with just simple Unix pipes.
Examples of such pipes, tools to calculate these identifiers, and index
file versions of the databases posted are being made available.

Other new identifiers, such as the IUPAC/NIST INChI, are also included for
all compounds on this site.  Cross-indexing with other web sites offering
large collections of public structures, such as NCBI's PubChem project and
the ZINC collection provided by the Shoichet Laboratory at UCSF is planned
as soon as it becomes technically feasible.

If you are interested in beta-testing the site while it is still evolving,
please send me e-mail and I will send you the URL.  Please be prepared for
problems ranging from minor annoyances to complete uselessness for your
particular purpose, as well as with the data themselves possibly still
changing.  Any feedback will be highly welcome.

Marc

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 Marc C. Nicklaus, Ph.D.                 NIH/NCI at Frederick
 E-mail: mn1~at~helix.nih.gov               Bldg 376, Rm 207
 Phone:  (301) 846-5903                  376 Boyles Street
 Fax:    (301) 846-6033                  FREDERICK, MD 21702      USA
            Head, Computer-Aided Drug Design (CADD) Group
     Laboratory of Medicinal Chemistry, Center for Cancer Research,
 National Cancer Institute at Frederick, National Institutes of Health
       http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm
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