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) 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 (1 st 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). 1 st ChemInt conference in Irvine, CA (Bachrach, Rzepa, Steve Heller). 1999: CML proposed (Rzepa, Murray-Rust). 2 nd ChemInt conference, Georgetown University. 2000: 3 rd ChemInt conference, Georgetown University. (time line provided courtesy of Steven Bachrach)

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