Subject: Announcement: Enhanced NCI Open Database Browser Release 2

From: "M. Nicklaus" <[email-masked]>
Date: Wed, 7 Feb 2001 19:04:44 -0500 (Eastern Standard Time)

The Erlangen/Bethesda Data Services, a collaboration between the CADD
Group of the Laboratory of Medicinal Chemistry, NCI, NIH, and the
Computer Chemistry Center at the University of Erlangen-Nuremberg, 
are pleased to announce Release 2 of the Enhanced NCI Database Browser 
for public beta testing.

This service, based on the chemical information toolkit CACTVS, offers
searches in the public dataset of over 250,000 open NCI database
compounds.

Numerous new features have been implemented, approx. 4,000 structures
added, and a very large number of additional data calculated and added to
the database of searchable information.

Here is a *partial* list of the new features and improvements:

- New GUI (window switching instead of multiple windows) 
- Continuation of search now possible if end of database was not reached 
- Hit list manager to store, intersect, add, subtract etc. hitlists
- New substructure search capabilities (e.g., search for H-bond
  acceptor/donor)  
- Many more, and/or improved, searchable criteria (log P [calc.],
  complexity, data availability...)
- Names added for approx. 220,000 structures (w/ ACD/Name; thanks to
  ACD/Labs) 
- PASS activity spectrum predictions (>500 mechanisms of action; most
  compounds; Prof. Vladimir Poroikov, Russ. Acad. Med. Sci., Moscow).
  These are more than 64,000,000 searchable data items.
- Links to additional other services for further processing of search
  results 
        - PubMed 
        - NTP 
        - NIST WebBook 
        - COMPARE 
	- ChemFinder
        ....and others 
- Additions and improvements to the output features 
        - MDL Chime for structures, conformers, and hitlists 
        - 3D Java Viewer 
        - VRML Scene 
        - Several spreadsheet formats for hitlists 
- Additional data can now be exported together with the structures,
  e.g. in an SD file with added fields
- SMILES output is now Unique SMILES (Daylight, JCICS 1989) 
- 3D pharmacophore search, in up to 25 conformers per compound

The site is fully functional, i.e. all data are available, and all search
funtionality has been implemented.  The current beta testing period is
intended to allow for bug fixes, polishing of the interface and help/FAQ
texts, and implementation (possibly) of minor changes requested by users
(althought we don't want to *promise* anything in this regard).

Although the Help page is not yet fully finished, it already contains a
lot of useful information.  Please have a look at it to learn about the
things you can do with the new service.

The raw files used to build this service are downloadable from this site
in SD and SMILES formats.

Also available, at either mirror, are several additional services that
people may find useful.

The URLs for the service are:
  http://cactus.nci.nih.gov (U.S. mirror)
  http://www2.ccc.uni-erlangen.de/ncidb2 (German mirror)

Please let us know what your experiences are with these services, positive
or negative.

(Note pertaining to the recent discussion of "Linux 2.4.0 and 2 GB
problem" on the CCL:  The new database file is about 3.5 GB.  
Therefore, on the U.S. mirror (a Linux box), a 2.4.0 kernel was necessary.  
After some performance problems experienced with the use of the mmap64()
system call, work-arounds both in the program and the data structures
have solved this problem.  Note that this is on an ext2 file system, not
on xfs or ReiserFS.  See also the separate posting by Wolf-Dietrich
Ihlenfeldt on this subject.)

Dr. Wolf-D. Ihlenfeldt
Computer Chemistry Center, Institute for Organic Chemistry,
University of Erlangen-Nuremberg
Naegelsbachstrasse 25, D-91052 Erlangen (Germany)
Tel (+49)-(0)9131-85-26579  Fax (+49)-(0)9131-85-26566
http://www2.ccc.uni-erlangen.de/wdi/

  and

------------------------------------------------------------------------
 Marc C. Nicklaus                        National Institutes of Health
 E-mail: [email-masked]               Bldg 376, Rm 207
 Phone:  (301) 846-5903                  376 Boyles Street
 Fax:    (301) 846-6033                  FREDERICK, MD 21702       USA
      http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm
  Laboratory of Medicinal Chemistry, National Cancer Institute, FCRDC
------------------------------------------------------------------------