Welcoming Remarks

1
Welcoming Remarks and a Very Brief History of
U.S. Govt. Chemical Databases and Open Chemistry

• Marc C. Nicklaus
• Computer-Aided Drug Design Group
• Chemical Biology Laboratory, NCI-Frederick, NIH,
  DHHS

2
Categories of Open Chemistry

• 1. Databases and websites E.g. NCI Open
  Database, Binding DB, PubChem, Chemspider, ChEMBL
  etc.
• 2. Software tools E.g. JME, RDKit, CDK,
  OpenBabel, KNIME etc.
• 3. Methods, standards, and definitions E.g.
  InChI, CML, ToxML etc.
• 4. Publications E.g. Internet Journal of
  Chemistry, Chemistry Central Journal, Journal of
  Cheminformatics etc.

3
Early Efforts (before 2000) at NIH, NIST

• NLM, NIH
• computerized databases in toxicology were made
  available to the public since 1967 (Wexler,
  Toxicology 157 (2001) 310)
• Toxnet Developed 1985 on the Web 1998
• PubMed Jan.1996 ? present. Precursors
  (fee-based)
• Chemline (Elhill text based) 1974 to 1997
• ChemID (Elhill text based) 1990 to 2000
• ChemIDlus 1998 ? present
• NCI, NIH
• DTP release of Open NCI Database (127k
  structures) Nov. 1994
• NCI Database Browser (246k), public beta (CCL)
  May 28, 1998
• (1st version by W.-D. Ihlenfeldt at CCC
  Erlangen, Oct. 1997)
• NIST NIST Chemistry Webbook Aug. 1996

4
Early Efforts (before 2000), non-database

• 1994 First chemistry web sites appear (Henry
  Rzepa at Imperial College, Steven Bachrach at
  Northern Illinois).
• First Electronic Computational Chemistry
  Conference ECCC, continue for another 9 years
  (Bachrach).
• 1995 Chemical MIME type proposed (Rzepa, Peter
  Murray-Rust).
• First Electronic Conference on Heterocyclic
  Chemistry (Rzepa).
• 1996 "The Internet A Guide for Chemists"
  published by ACS Publications (Bachrach, editor).
• 1998 "Internet Journal of Chemistry
  (1998-2004), Bachrach, editor in chief.
• MDL releases Chime.
• JME released (Peter Ertl).
• 1st ChemInt conference in Irvine, CA (Bachrach,
  Rzepa, Steve Heller).
• 1999 CML proposed (Rzepa, Murray-Rust).
• 2nd ChemInt conference, Georgetown University.
• 2000 3rd ChemInt conference, Georgetown
  University.
• (time line provided courtesy of Steven Bachrach)

5
Previous Meetings on U.S. Govt. Chemical Databases

• Date Number of participants
• August 11, 2000 () 23
• December 12, 2000 25
• July 21-22, 2003 46
• July 12-13, 2005 70 ( 5 panel members)
• () Informal Meeting on Public Govt. Chemical
  Databases

6
Databases, Tools, Projects - 1999 to date

• JChemPaint - 1999
• Chemistry Development Kit - 2729 September 2000
• Binding DB 2001
• OpenBabel 2001
• NIAID ChemDB HIV/AIDS Database 2002
• Ligand Depot November 2003 (first protein
  structure with a ligand in PDB released 1976)
• ZINC database 2004
• PDBbind database - 2004
• PubChem 2004
• sc-PDB - 2004
• Binding MOAD 2004
• DrugBank - 2005
• Blue Obelisk 2005
• Chemical Structure Lookup Service (CSLS)
  September 2006
• ChemSpider March 2007
• ChEMBL 2008/2009
• Chemical Identifier Resolver (CIR) July 2009

7
Players missing (at this meeting)

• ...among others
• Google
• U.S. PTO
• U.S. DoD groups, such as Walter Reed (Malaria
  database)

8
Acknowledgments

• These Slides
• Steven Bachrach
• George Mike Hazard
• Dan Zaharevitz
• Meeting Organization
• Julia Lam
• The CADD Group Team Igor Filippov, Megan Peach,
  Markus Sitzmann