Embed Size (px)
Citation preview
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
N
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
Buy onlineYou may purchase this article in PDF and/or HTML formats. For
purchasers in the UK, and for purchasers elsewhere in the European Community who do not have a VAT number, VAT will be added to the price of the article.
Format* PDF (US $40, plus US $7 for EC purchases)
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
$$$$
Yokoyama dataset
Search Genbank for “aattccgg”
C
C
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
T
O
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
N
O
NCl
H2N
O
H2N
H2N
HN
N
N
Cl
HN
N
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
