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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. Welcoming Remarks – and a Very Brief History of U.S. Govt. Chemical Databases and Open Chemistry. Categories of “Open Chemistry”.

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

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  1. Marc C. Nicklaus Computer-Aided Drug Design Group Chemical Biology Laboratory, NCI-Frederick, NIH, DHHS Welcoming Remarks – and a Very Brief History of U.S. Govt. Chemical Databases and Open Chemistry

  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) 3–10) • 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- 27–29 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

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