1. How to use DiscoveryGate 2.3 An introduction to using DiscoveryGate Presented By: Doreen Tan, PSM, Elsevier S&T (APAC) Presentation dates: 12 & 13 November 2007

2. 2 Agenda  What is DiscoveryGate?  Setting up DiscoveryGate on your machine  DiscoveryGate homepage orientation  Using MDL Draw (live demo)  Molecule/Structure search (live demo)  Individual Database search (live demo)  Create reports (live demo)  Reaction search with data query (live demo)  Questions

3. 3 What is DiscoveryGate?  A web-based portal to 17 premier complementary databases and reference works in Chemistry  More than 21 million compounds  More than 14 million reactions  More than 550 million searchable facts & data as reported in literature  Allows one-query access to over synthesis, bioactivity, physical property and sourcing databases.  Links to over 15,000 journals and patent archives  Designed to increase the productivity of drug discovery process  Unlimited access 24/7

4. 4 Bioactivity MDL Data Drug Report MDL Metabolite Database MDL Toxicity Database National Cancer Institute Databases MDL Comprehensive Medicinal Chemistry xPharm** PharmaPendium** Patent sources Derwent World Patent Index* Integrated Major Reference Works Comprehensive Asymmetric Catalysis (CAC) Comprehensive Organic Functional Group Transformation (COFGT) Chemistry Reference CrossFire Beilstein (not indexed in Compound Index) CrossFire Gmelin (not indexed in Compound Index) MDL® Patent Chemistry Database** OHS Pure Substance MSDS Database** ISI Index Chemicus* Synthetic Methodology ChemInform Reaction Library Current Synthetic Methodology Derwent Journal of Synthetic Methods ORGSYN Database MDL Solid-Phase Organic Reactions MDL Reference Library of Synthetic Methodology ISI Current Chemical Reactions* Chemical Sourcing and Logistics MDL Available Chemicals Directory MDL Screening Compounds Directory * = 3 rd party databases. Structures are indexed in Compound Index. Users need to link out to 3 rd party application to view detailed data. Access depends on individual institution’s subscription with the 3 rd party. ** = Not included in the A&G package but can be added on at additional license fee. What is DiscoveryGate (cont)?

5. 5 What can DiscoveryGate do?

6. 6 New license will include access to full Beilstein database Click to open Pharmacological and Ecological data (5 fields) Current license provided access to Beilstein Abstracts New license provides access to full Beilstein database Click to open Pharmacological and Ecological data (>100 fields)

7. 7 Search structures and reactions  Select a database and perform a structure and property search  Returns data from multiple databases with a single search  Click directly into primary databases for more detail

8. 8 Indexed relationships shown directly  This compound found in 11 databases  Click any link to see detailed record(s)

9. 9 Extend research to the full text  Get better value from existing subscriptions by linking automatically from citations to corresponding full text and patents.  Librarians can:  Manage links on DiscoveryGate or  Point to internal library link resolver Users can export references to Reference Management tools such as EndNote All bibliographic AND patent references are hyperlinked

10. 10 Collect, organize, and share data DiscoveryGate allows scientists to create and share custom reports with data extracted from the literature

11. 11 DiscoveryGate LIVE www.discoverygate.com

12. 12 DiscoveryGate homepage

13. 13 MDL Database Browser (DBB) Database selection drop down menu

14. 14 MDL Database Browser (DBB)  Each tab has its default page and function:  Queries tab – for formulation & executing query  Results tab – displays hit list and results of your query  Reports tab – for creating reports of your searches.

15. 15 Using MDL Draw  Lasso  Rotate/Flip  Zoom/Pan  Eraser  All Purpose Drawing tool  Atom  Properties  Single bong  Chain  Up wedge  Functional Groups

16. 16 DIY Exercise 1 – Draw Phenylbutazone

17. 17 Search Types Exact : Search for substances that match your structural query exactly. Include Tautomers : Search for tautomers, and also for structures with different charges and different isotopes. Include Isomers : Search for stereoisomers (all R and S orientations, all E & Z configurations and so on). Include Salts : Search for substances that include different salts. Substructure : Search for substances that contain your query wholly embedded within them. Similarity : Search for substances that are structurally similar to your query.

18. 18 Database Abbreviations AbbreviationDatabase BeilsteinCrosssFire Beilstein GmelinCrossFire Gmelin ACDAvailable Chemicals Directory SCDScreening Compounds Directory CCRISI Current Chemicals Reactions* DWPIISI Derwent World Patent Index* Index ChemicusISI Index Chemicus* CIRXChemInform Reaction Library CSMCurrent Synthetic Methodology DJSMDerwent Journal of Synthetic Methodology RefLibMDL Reference Library NCINational Cancer Institute DBORGSYN MetaboliteMDL Metabolite DB ToxicityMDL Toxicity DB SPOREMDL Solid-Phase Organic Reactions CMCComprehensive Medicinal Chemistry MDDRMDL Drug Data Report

19. 19 Substructure + Data Search

20. 20 DIY Exercise 2 1. Conduct an exact match search for beta-aminopyridine in the MDL Compound Index. 2. View the results 3. Search for compounds that contain the beta-aminopyridine substructure, including isomers, and have molecular weight less than 150. 4. View the results. How do they differ from the results from the exact match search?

21. 21 Data Searching in Individual Databases  Each database has its own predefined search forms.  Search forms are stored in “Easy Data Search” folder

22. 22 Each database has its default query form  Each database has a defined default query form.  CrossFire Beilstein and CrossFire Gmelin has predefined forms stored in the Easy Data Search  The forms can be modified.

23. 23 Using Data Fields and Operators

24. 24 Data Operators & Wild Cards

25. 25 DIY Exercise 3 – Acyclovir in Beilstein  Acyclovir, CAS number 59277- 89-3  Do two searches: 1 st by name, then another search by CAS number  Compare the results

26. 26 “BIO” label  The “ BIO ” label indicates that the compound has pharmacological or toxicological information associated with it.

27. 27 Creating a report  In results tab, click on “copy to report”  Specify range of records to copy to report  Check “view report now”  A report will be a copy of your selected results without the hyperlinks.

28. 28 DIY Exercise 4 –  Search ACD database for compound with CAS Registry number 719-64-2. View suppliers and prices for the compound.  Make a report of the prices.  Conduct a name search for “Atrazine” in the CrossFire Beilstein Database.  View pharmacological data for one compound; retrieve one of the literature references.

29. 29 Reaction Searching  2 groups of reactions databases: CrossFire Beilstein and Synthetic Methodology Information  You can select individual databases under Synthetic Methodology Information.

30. 30 Drawing Reaction using MDL Draw

31. 31 Substructure Reaction Search

32. 32 DIY Ex. 5 – Substructure Reaction Search  Retrieve reactions that include 6-nitro-nicotinic acid as a product.  View details of one reaction, and find a synthetic pathway.

33. 33 Setting up DiscoveryGate Minimum System Requirements On PCsOn Macintoshes Hardware Processor Speed RAM Intel-compatible Pentium III or better 1000MHz or higher RAM 512 MB < (PowerPC) G4 or higher Any Intel version 800 MHz or higher RAM 512 MB < SoftwareMS Windows 2000 SP4 or MS Windows XP SP1 JRE: 1.4.2_06 or 1.5.0 Internet Explorer 6.0 SP1 or higher Adobe Acrobat Reader 8.0 or higher Mac OS 10.4 or higher Safari 2.0 or higher Adobe Acrobat Reader 8.0 or higher.

34. 34 Setting up DiscoveryGate  Download the DiscoveryGate installer http://www.discoverygate.com/DiscoveryGate23sp2sr1.exe  Install it  make sure you have administrative privileges  and that all IE windows are closed. Otherwsie the install wizard will abort.  Re-open IE, click OK when prompted for Java update.  Unblock site in pop-up blocker

35. 35 Setting up DiscoveryGate Step 1 – Run the DiscoveryGate installer  Go to www.discoverygate.com  Download the DiscoveryGate installer  Make sure you have administrative rights to the machine  Run DiscoveryGate installer (All other IE windows must be closed).  Installer will automatically close IE when installation has completed.

36. 36 Setting up DiscoveryGate (contd) Step 2 --- Have the correct Java Runtime Environment  Relaunch IE and go to URLwww.discoverygate.com  JAVA update will run automatically if you do not have the appropriate version.  The structure search box appears clear if you have the correct Java Runtime Environment

37. 37 Setting up DiscoveryGate (contd) Step 3 --- Disable Pop-up Blocker  Double click on application “Search Database”  If you get a “pop-up blocked” message, right click on the yellow bar on top and select “always allow…”  Click “Yes” when prompted

38. 38 Questions? Thank you! Doreen Tan Product Sales Manager, Life Science Elsevier S&T (ANZ, SEA, Taiwan) D.Tan@elsevier.com +65 63490212