Klaus Gubernator, Craig James, eMolecules Inc.

ACS 232nd National Meeting

Division of Chemical Information

  San Francisco, September 14, 2006

Chemical Structure Search Engines in Cyberspace

The web has revolutionized the way we retrieve information

Chemistry is a late participant in this revolution

Chemistry on the Internet

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Search Google Images for “Aspirin”

http://scripts.iucr.org/cgi-bin/paper?cnor=a12172&buy=yes

Acta Cryst. (1975). B31, 1427-1429    The crystal structure of 7-amino-2H,4H-vic-triazolo[4,5-c]-1,2,6-

thiadiazine 1,1-dioxide (ATT)C. Foces-Foces, F. H. Cano and S. García-Blanco

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Structure of “triazolo thiadiazine”

Datasets (which are, in contrast to other dataset lists, available in a structural format)This list will be expanded continuously. Please don't hesitate to make published datasets publicly available here.

Currently available: 44 DatasetsNote: The Briem/Lessel and Hert/Willett Dataset are only available as MDDR ID's due to license reasons. Please contact MDL for further information on the database. The datasets have nonethless been included here because they are standard datasets for similarity searching. – Andreas Bender

Binary (active/inactive) datasets QSAR datasets QSPR datasets Toxicity datasets Metabolism datasets Permeability datasets Docking datasets Mechanistic datasets Mixed/Other datasets

Cheminformatics.org

CS(=O)(=O)Nc1ccc(cc1OC2CCCCC2)N(=O)=OCS(=O)(=O)Nc1cc2CCC(=O)c2cc1Oc3ccc(F)cc3FCS(=O)(=O)Nc1cc2CCC(=O)c2cc1Sc3ccc(F)cc3FCS(=O)(=O)Nc1ccc(cc1Sc2ccc(F)cc2F)C(=O)NCS(=O)(=O)Nc1ccc(cc1Sc2ccc(Cl)cc2Cl)S(=O)(=O)NCOc1ccc(cc1)c2sc(nc2c3ccc(cc3)S(=O)(=O)C)c4ccccc4ClCOc1ccc(cc1)c2sc(nc2c3ccc(SC)cc3)c4ccccc4ClCS(=O)(=O)c1ccc(cc1)n2nc(cc2c3ccc(F)cc3)C(F)(F)FCS(=O)(=O)c1ccc(cc1)n2nc(cc2c3ccc(Br)cc3)C(F)(F)FCc1ccc(cc1)c2cc(nn2c3ccc(cc3)S(=O)(=O)N)C(F)(F)FCS(=O)(=O)c1ccc(cc1)c2snnc2c3ccc(F)cc3CC(=O)c1nc(c(o1)c2ccc(c(F)c2)S(=O)(=O)N)c3ccccc3Cc1nc(C2CCCCC2)c(o1)c3ccc(c(F)c3)S(=O)(=O)NCS(=O)(=O)c1ccc(cc1)c2[nH]c(nc2C3CCCCC3)C(F)(F)FCS(=O)(=O)c1ccc(cc1)c2[nH]c(nc2c3ccc(F)cc3)C(F)(F)FCS(=O)(=O)c1ccc(cc1)C2=C(C(=O)OC32CC3)c4ccccc4CS(=O)(=O)c1ccc(cc1)C2=C(C(=O)OC32CCCC3)c4ccccc4CS(=O)(=O)c1ccc(cc1)c2cnn(Cc3ccccc3)c(=O)c2c4ccccc4CS(=O)(=O)c1ccc(cc1)c2nn(Cc3ccccc3)c(c2c4ccc(F)cc4)C(F)(F)FNS(=O)(=O)c1ccc(cc1)c2c(CO)onc2c3ccccc3CS(=O)(=O)c1ccc(cc1)c2cc(Cl)nn2c3ccc(F)cc3NS(=O)(=O)c1ccc(cc1)c2cc(nn2c3ccc(F)cc3)C(F)(F)FNS(=O)(=O)c1ccc(cc1)n2nc(cc2c3nc4cccc(F)c4s3)C(F)F

Stahl dataset

Unnamed -MTS- 06200418093D 0 0.00000 0.00000 0

13 13 0 0 0 0 0 0 0 0 1 V2000 0.0180 -0.0030 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 1.7880 0.0070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4880 0.0110 1.2120 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8880 0.0200 1.2120 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5880 0.0240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0030 0.0330 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.6610 1.1880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0400 2.2500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.1410 1.1970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7570 0.1440 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.7890 2.3360 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8880 0.0200 -1.2130 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4880 0.0120 -1.2120 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 …M END> <BIO>48.00

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Yokoyama dataset

Search Genbank for “aattccgg”

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Why is so little chemistry on the web?

Tradition? Strong providers of subscription services? Searching for chemical structures is

significantly more difficult than text searching?

Chemical identifiers are not standardized?

Open Access Chemical Search Engines

PubChem - NIH

ChemBank – Harvard

ZINC – UCSF

ChemDB – UC Irvine

ChemExper - Lausanne

ChemFinder – CambridgeSoft

www.emolecules.com

New Chemistry Search Engine A large database of publicly available

molecular structures Launched November 2005 50,000 searches per month, rapidly

growing

www.emolecules.com

Free chemistry search site for publicly available chemical information

Advanced Search

Powerful features: hit list management union, intersect, subtract, difference manual selection export lists in many formats persistent hitlists

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Content: 16M entries, 5.6M structures

Academic and government databases NIST WebBook DrugBank Protein Ligands

Chemical suppliers 150 electronic catalogs included

Future goal All publicly available chemical information

Why is it so fast?

Novel chemical search engine technology

Method represents a major departure from previously known algorithms- Molecular keys (MDL)

- Fingerprints (Daylight)

- Feature Trees (BioSolv)

Search engine technology

Analyze each molecule for distinguishing structural features

Generate all features algorithmically

Normalize features and use them for indexing

Result: very fast searches

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NCl

H2N

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H2N

H2N

HN

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Who is eMolecules?

Klaus Gubernator

Craig A. James

Rashmi Mistry

Summary

Free for depositors and users Very fast search engine High quality user interface Rich functionality Complementary with other engines

Contact Information

Klaus Gubernator

klaus@emolecules.com

Skype: emolecules

+1-858-764-1941