How to use DiscoveryGate 2.3An introduction to using DiscoveryGate

Presented By: Doreen Tan, PSM, Elsevier S&T (APAC)Presentation dates: 12 & 13 November 2007

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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

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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

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BioactivityMDL Data Drug ReportMDL Metabolite DatabaseMDL Toxicity DatabaseNational Cancer Institute DatabasesMDL Comprehensive Medicinal ChemistryxPharm**PharmaPendium**

Patent sourcesDerwent World Patent Index*

Integrated Major Reference WorksComprehensive Asymmetric Catalysis (CAC)Comprehensive Organic Functional Group

Transformation (COFGT)

Chemistry ReferenceCrossFire 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 MethodologyChemInform Reaction LibraryCurrent Synthetic MethodologyDerwent Journal of Synthetic MethodsORGSYN DatabaseMDL Solid-Phase Organic ReactionsMDL Reference Library of Synthetic MethodologyISI Current Chemical Reactions*

Chemical Sourcing and LogisticsMDL Available Chemicals DirectoryMDL Screening Compounds Directory

* = 3rd party databases. Structures are indexed in Compound Index. Users need to link out to 3rd party application to view detailed data. Access depends on individual institution’s subscription with the 3rd party. ** = Not included in the A&G package but can be added on at additional license fee.

What is DiscoveryGate (cont)?

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What can DiscoveryGate do?

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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)

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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

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Indexed relationships shown directly

This compound found in 11 databases Click any link to see detailed record(s)

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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

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

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DiscoveryGate LIVE

www.discoverygate.com

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DiscoveryGate homepage

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MDL Database Browser (DBB)

Database selection drop down menu

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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.

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Using MDL Draw

Lasso Rotate/Flip Zoom/Pan Eraser All Purpose Drawing tool Atom Properties Single bong Chain Up wedge Functional Groups

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DIY Exercise 1 – Draw Phenylbutazone

N

N

O

O

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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.

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Database AbbreviationsAbbreviation DatabaseBeilstein CrosssFire BeilsteinGmelin CrossFire GmelinACD Available Chemicals DirectorySCD Screening Compounds DirectoryCCR ISI Current Chemicals Reactions*DWPI ISI Derwent World Patent Index*Index Chemicus ISI Index Chemicus*CIRX ChemInform Reaction LibraryCSM Current Synthetic MethodologyDJSM Derwent Journal of Synthetic MethodologyRefLib MDL Reference LibraryNCI National Cancer Institute DBORGSYN ORGSYNMetabolite MDL Metabolite DBToxicity MDL Toxicity DBSPORE MDL Solid-Phase Organic ReactionsCMC Comprehensive Medicinal ChemistryMDDR MDL Drug Data Report

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Substructure + Data Search

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NN

DIY Exercise 21. 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?

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Data Searching in Individual Databases Each database has its own

predefined search forms. Search forms are stored in

“Easy Data Search” folder

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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.

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Using Data Fields and Operators

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Data Operators & Wild Cards

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DIY Exercise 3 – Acyclovir in Beilstein Acyclovir, CAS number 59277-

89-3 Do two searches: 1st by name,

then another search by CAS number

Compare the results NN

NN

O

O

N

O

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“BIO” label

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

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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.

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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.

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Reaction Searching 2 groups of reactions

databases: CrossFire Beilstein and Synthetic Methodology Information

You can select individual databases under Synthetic Methodology Information.

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Drawing Reaction using MDL Draw

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Substructure Reaction Search

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N+

N

O-

O

O O

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.

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Setting up DiscoveryGateMinimum System Requirements

On PCs On Macintoshes

Hardware

Processor SpeedRAM

Intel-compatible Pentium III or better1000MHz or higherRAM 512 MB <

(PowerPC) G4 or higherAny Intel version800 MHz or higherRAM 512 MB <

Software MS Windows 2000 SP4 orMS Windows XP SP1JRE: 1.4.2_06 or 1.5.0Internet Explorer 6.0 SP1 or higherAdobe Acrobat Reader 8.0 or higher

Mac OS 10.4 or higher

Safari 2.0 or higherAdobe Acrobat Reader 8.0 or higher.

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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

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Setting up DiscoveryGateStep 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.

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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

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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

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Questions?Thank you!

Doreen TanProduct Sales Manager, Life ScienceElsevier S&T (ANZ, SEA, Taiwan)D.Tan@elsevier.com

+65 63490212