The collaboration enables researchers to identify drug targets and bioactive compounds via pathway analysis and retrieve comprehensive information on their synthesis, biological effects and commercial availability without having to re-query for it. "For the first time, biologists will be able to quickly review cheminformatics data of small molecules involved in biological pathways, and chemists will be able to view molecular pathway information related to their lead compounds."

1. lsevier MDL and GeneGo have
linked databases to make it easier
and quicker for researchers to
access more information without repeating
searches in multiple diverse platforms. The
GeneGo databases for systems biology
and pathway analysis (MetaCore™
and
MetaDrug™
) are now linked with the
synthesis, sourcing and bioactivity data-
bases on the DiscoveryGate®
platform.
MetaCore is a unique, curated database
of human protein-protein and protein-DNA
interactions, transcription factors, signaling
and metabolic pathways and the effects
of bioactive molecules. MetaDrug is a
systems pharmacology platform that
predicts human drug metabolism, potential
toxicities and mode of action for novel
small molecules.
The collaboration enables researchers
to identify drug targets and bioactive
compounds via pathway analysis and
retrieve comprehensive information on
their synthesis, biological effects and
commercial availability without having
to re-query for it.
“The integration of MDL databases
with GeneGo’s pathways information
systems enables scientists to bridge the
gap between cell biology and medicinal
chemistry,” says Steve Young, Director
of MDL Content Strategy. “For the first
time, biologists will be able to quickly
review cheminformatics data of small
molecules involved in biological pathways,
and chemists will be able to view molecular
pathway information related to their
lead compounds.”
“Lately, a number of customers
approached us with requests for functional
analysis of the effects of drug-like com-
pounds rather than genomic data,” says
Julie Bryant, VP Business Development
at GeneGo. “Although pathways and
network analysis of bioactive compounds
is a common practice in MetaCore, we
partnered with Elsevier MDL for in-depth
coverage of literature- and patent-derived
information relevant for compounds.
We are very pleased to be working with
Elsevier MDL, the market leader in
medicinal chemistry factual databases.
Integration with the Elsevier MDL chemistry
space opens up new applications for
our products in medicinal chemistry,
including high-throughput and high-
content screening, hit selection and
validation, lead development programs
and chemogenomics.”
Reprint from Molecular Connection Vol 24 No 4 2006
Collaboration with GeneGo provides
seamless access to compound databases,
patents, literature and biological pathways
GeneGo develops systems biology technology for life
sciences research. The original computational platform
allows an integration and expert analysis of different
kinds of experimental data (mRNA expression,
proteomics, metabolomics, siRNA and other phenotypic
data) and relevant bioactive chemistry (metabolites, drugs, other xenobiotics) within
the framework of curated biological pathways and networks. GeneGo’s flagship
product, MetaCore, assists pharmaceutical scientists in the areas of target selection
and validation, identification of biomarkers for disease states and toxicology. MetaDrug
is designed for prediction of human metabolism, toxicity and biological effects for
novel small molecules compounds. MetaBase™
represents the knowledge base
for MetaCore. For more information about GeneGo products and services, please
visit www.genego.com.
About GeneGo
“For the first time, biologists will be able to quickly
review cheminformatics data of small molecules
involved in biological pathways, and chemists will be
able to view molecular pathway information
related to their lead compounds.”
E

2. Reprint from Molecular Connection Vol 24 No 4 2006
You want to study related pharmaco-
logical information (e.g., adverse effects,
toxicity, dose response curves, primary
literature, etc.) on Celecoxib, a known
COX-2 inhibitor.
In GeneGo you conduct a signaling
networks search on Celecoxib which
builds a network mapping the relation-
ship between this compound and
targets/receptors.
Figure 1: The Celecoxib molecule is shown in the network diagram (purple hexagon, circled).
Double-click on the Celecoxib purple
hexagon to open the ‘Chemical compound
details’ display.
The default search type when transferring
a structure to DiscoveryGate is automatic
search. The system looks for records that
match the query using the following
search types in this order: exact match,
include isomers, include tautomers, include
salts, substructure, similarity (90%) and
similarity (70%), until at least one hit is
found. Each search is somewhat more
general than the preceding search.
Select substructure as the search
method to receive all substances that
contain the Celecoxib core structure and
then click on Search in DiscoveryGate
to transfer this structure to the MDL®
Compound Index (license to DiscoveryGate
required).
In addition to target information from
MetaCore you get pharmacology, safety,
toxicity, adverse effort and metabolism
data, as well as commercial availability
and preparation data via DiscoveryGate.
Select Details on the Celecoxib
record to see all related records available
via the Compound Index.
Figure 2: Celecoxib compound details. A reaction in GeneGo nomenclature is equivalent to a
metabolic transformation in MDL databases.
1
2
Figure 3: The ‘Grid View’ (background) allows you to quickly see all related structures containing
the Celecoxib core structure. The ‘Properties View’ (foreground) shows related records in a
properties context.
3
1
2
The integration of MDL
databases with GeneGo’s
pathways information
systems bridges the gap
between cell biology and
medicinal chemistry.

3. Reprint from Molecular Connection Vol 24 No 4 2006
Figure 4: DiscoveryGate provides “Also found in” links at the top of each record offering
immediate connections to relevant information on the same compound in other data sources.
45
Figure 5: xPharm and PharmaPendium record displays for Celecoxib (xPharm and PharmaPendium
licenses required).
Figure 6: Information in PubChem is categorized based on the Medical Subject Heading
(MeSH) indexing schema.
6
This record for Celecoxib includes direct
links to the GeneGo databases, that is,
bidirectional linking is enabled (MetaCore
and/or MetaData licenses required).
Click on xPharm®
and PharmaPendium™
in the ‘Also found in’ links to access a
wealth of pharmacological and adverse
effects information on Celecoxib.
Click on PubChem in the ‘Also found
in’ links to access bioassay data.
Select PubMed via MeSH to access
associated biological and pharmacological
effect information from the corresponding
primary literature.
DiscoveryGate and the MDL®
Compound Index
The online DiscoveryGate platform
(www.discoverygate.com) provides
access to integrated scientific con-
tent from databases, journal articles,
patent publications and reference
works from information providers
including Elsevier, Thomson-Derwent,
FIZ CHEMIE, the USFDA, Prous
Science and Thieme.
With the addition of chemical
structures from the GeneGo data-
bases, MetaCore and MetaDrug,
the MDL Compound Index (the
master list of substances included
in DiscoveryGate data sources)
now exceeds 16.5 million unique
chemical structures. Altogether, more
than 22 million unique structures are
accessible via DiscoveryGate.
4
5
6
The collaboration with
GeneGo expands the network
by enabling researchers to
link from molecules in
GeneGo’s biological
pathways to DiscoveryGate
to find related information.

4. Indexing third-party data in the
Compound Index extends the network
of platforms interlinked via DiscoveryGate
and provides researchers with unified,
simple access to a wealth of related data.
The GeneGo linking was made possible
by using the ‘Send-To’ mechanism,
which enables the transfer of chemical
structures from in-house or third-party
applications directly to DiscoveryGate
via a single click in the application.
The chemical structure is converted
to a Chimestring in the GeneGo
application via a dynamic molfile-to-
Chimestring conversion (using classes
in csinline.jar). The researcher selects
the search type (e.g., automatic, exact,
substructure, include stereoisomers,
include tautomers and include salts).
When the researcher clicks on the
trigger point, the Chimestring and the
search type are placed on a hidden Web
form which is sent to DiscoveryGate.
The ‘Send-To’ mechanism can be
implemented in customer proprietary
applications (COM, .net, Java).
‘Send-To’ mechanism makes
GeneGo integration possible
Reprint from Molecular Connection Vol 24 No 4 2006
MDL, DiscoveryGate and PharmaPendium are registered trademarks or trademarks of MDL Information Systems, Inc. ('Elsevier MDL')
in the United States and/or other countries. MetaCore, MetaDrug and MetaBase are trademarks of GeneGo, Inc. xPharm is a registered
trademark of Elsevier, Inc. in the United States and other countries. ScienceDirect is a registered trademark of Elsevier B.V. All other
product and company names mentioned herein may be trademarks or registered trademarks of their respective holders.
Copyright © 2006 Elsevier MDL. All rights reserved.
Elsevier MDL
2440 Camino Ramon,
Suite 300
San Ramon,CA 94583
Tel: +1(925) 543-5400
Fax: +1(925) 543-5401
www.mdl.com
Figure 7: Celecoxib-related citations available in PubMed.
Figure 8: In ScienceDirect, scientists can read and print the published article in its entirety
(ScienceDirect license required).
More information
‘Send-To’ mechanism article from Molecular Connection (2005, Vol. 23, No. 3, page 10) and
this article are available as reprints (PDF). www.mdl.com/products/knowledge/discoverygate
See this case study as an interactive video. www.mdl.com/videos
Sign-up for a 30-day trial of DiscoveryGate (no fee, no obligation to buy, subject to acceptance
of the applicable DiscoveryGate Evaluation license). www.discoverygate.com
Read a review article about xPharm®
, reprinted from the Journal of Electronic Resources in Medical
Libraries, courtesy of The Haworth Press, Inc. www.mdl.com/products/pdfs/xpharm.pdf
With the addition of chemical structures from
the GeneGo databases, MetaCore and MetaDrug,
the MDL Compound Index now exceeds
16.5 million unique chemical structures.
Select Links > Linkout and Elsevier
MDL to access the full article on
ScienceDirect.
From its inception, DiscoveryGate has
provided researchers with focused informa-
tion, relevant to specific research questions,
from a network of indexed and linked data
sources. As the above scenario shows,
collaboration with GeneGo expands the
network by enabling researchers to link
from molecules in GeneGo’s biological
pathways (a display of networks around
proteins, genes and compounds) to
DiscoveryGate to find related information.
This integration will help researchers
find critical information while avoiding
unnecessary, repetitious searches of
multiple systems or data sources.
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