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SOMA2 – Drug Design Environment
Drug design environment – SOMA2
 The SOMA2 project 2002-2006
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Tekes (National Technology Agency of Finland) DRUG2000 program.
Organizes and updates CSC’s (the Finnish IT Center for Science) modeling program
environment to meet the standards in modern computer-aided molecular design.
Promotes the use of computing tools in drug discovery research work in Finland.
Provides easy access to computational tools through WWW – interface.
Integrates different tools, operates as middleware program.
Allows user to define unique computational workflow (pipeline, network etc.).
Drug design environment – SOMA2
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FROM MOLECULES …
… TO PROTEINS …
…AND CELL-LEVEL ACTIVITIES
 Software for ADME and structure-based drug discovery
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Databases of chemistry and protein structures and tools to analyze them
Docking and classification of molecules
QSAR (Quantitative Structural Analysis Research)
Computer-assisted high-throughput screening
Design of ligands
ADME predictions (Absorption, Distribution, Metabolism and Excretion), Toxicity
Data management, data mining and visualization
Drug design environment – SOMA2
INTERNET,
researcher’s PC
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CSC-network and Scientist interface,
SOMA2 environment
computing grid
 Basic technical concept
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Dock to target
protein
Convert to 3D
Calculate chemical
properties
Query database
GOLD on Linux
Corina on Solaris
Sybyl on Linux
ISIS on Solaris
WWW – interface is based on the XML –
description of a program.
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b) INPUT:
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Different machine architectures are hidden.
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Automatic generation of program and platform
specific configuration files.
2D structure,
known data
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SOMA2 environment
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CML
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CML (chemical markup language) is used as
internal data format (data transferred in XML).
ADME
prediction
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XML
2D > 3D
conversion
XML
Unique computational workflows.
OUTPUT:
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• 2D structure,
• 3D structure,
• original data,
• docking score,
• ADME-values
Docking
XML
Drug design environment – SOMA2
 Model workflow
Figure from:
Lehtovuori, P. Nyrönen, T., SOMA - Workflow for Small Molecule Property Calculations on a Multiplatform
Computing Grid, J. Chem. Inf. Model., 2006, 46(2), 620-625.
Drug design environment – SOMA2
 Generic user interface generation
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User interface generated from description that is based on XML schema (“template”).
No programming skills required to produce XML – description of a program.
• New programs are easily added to SOMA2 – environment.
Save expert user knowledge in XML.
 Flexibility
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Not only for cheminformatics and drug design.
SOMA2 – system can be applied in almost every application area.
 Open source thinking
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Similar products available usually they are commercial.
Although some of the programs used are commercial, SOMA2 system is planned to be open
source.
Drug design environment – SOMA2
 Model workflows
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User can choose a
predefined workflow
for specific task.
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Predefined workflow
can still be freely
modified.
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Possibility to save own
workflows as a
template.
Drug design environment – SOMA2
 Input molecules
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Upload files from local
computer.
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Sketch molecules
within the user
interface.
Drug design environment – SOMA2
 Database query
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MDL ISIS host
databases.
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Support for structure
search.
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Search results
imported to SOMA2 –
system or
downloaded.
Drug design environment – SOMA2
 Program configuration
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Easy configuration of
programs.
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Useful help texts and
reasonable defaults
included in program
XML.
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System includes
model templates for
running a program.
Drug design environment – SOMA2
 Workflow manager
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Free navigation
between steps.
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Insert, change and
delete operation
supported.
Drug design environment – SOMA2
 Result view
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Spreadsheet like
result view.
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Tools for sorting and
filtering data.
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Basic data analysis.
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Save molecular data
in different formats.
Drug design environment – SOMA2
 Result details
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Visualisation of the
result molecules.
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Summary of computed
properties.
Additional information
 CSC – the Finnish IT Center for Science
• http://www.csc.fi
 SOMA2 – project:
• http://www.csc.fi/proj/drug2000/index.phtml.en
Acknowledgements
 Tekes (National Technology Agency of Finland):
• http://www.tekes.fi
 ChemAxon Ltd.:
• http://www.chemaxon.com