SOMA2 – Drug Design Environment. Drug design environment – SOMA2 The SOMA2 project 2002-2006...
Transcript of SOMA2 – Drug Design Environment. Drug design environment – SOMA2 The SOMA2 project 2002-2006...
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SOMA2 – Drug Design Environment
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Drug design environment – SOMA2
The SOMA2 project 2002-2006• 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.).
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Software for ADME and structure-based drug discovery• 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
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FROM MOLECULES … … TO PROTEINS … …AND CELL-LEVEL ACTIVITIES
Drug design environment – SOMA2
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Query database
ISIS on Solaris
Calculate chemical properties
Sybyl on Linux
Convert to 3D
Corina on Solaris
Dock to target protein
GOLD on Linux
INTERNET,researcher’s PC
Scientist interface,SOMA2 environment
CSC-network andcomputing grid
SOMA2 environment O
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2D > 3Dconversion
ADMEprediction Docking
• 2D structure,• 3D structure,• original data,• docking score,• ADME-values
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2D structure,known data
INPUT:
OUTPUT:
CML
XML XML XML
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Drug design environment – SOMA2
Basic technical concept• WWW – interface is based on the XML –
description of a program.
• Different machine architectures are hidden.
• Automatic generation of program and platform specific configuration files.
• CML (chemical markup language) is used as internal data format (data transferred in XML).
• Unique computational workflows.
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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.
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Drug design environment – SOMA2
Generic user interface generation• 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• Not only for cheminformatics and drug design.
• SOMA2 – system can be applied in almost every application area.
Open source thinking• Similar products available usually they are commercial.
• Although some of the programs used are commercial, SOMA2 system is planned to be open source.
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Drug design environment – SOMA2
Model workflows• User can choose a
predefined workflow for specific task.
• Predefined workflow can still be freely modified.
• Possibility to save own workflows as a template.
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Drug design environment – SOMA2
Input molecules• Upload files from local
computer.
• Sketch molecules within the user interface.
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Drug design environment – SOMA2
Database query• MDL ISIS host
databases.
• Support for structure search.
• Search results imported to SOMA2 – system or downloaded.
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Drug design environment – SOMA2
Program configuration• Easy configuration of
programs.
• Useful help texts and reasonable defaults included in program XML.
• System includes model templates for running a program.
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Drug design environment – SOMA2
Workflow manager• Free navigation
between steps.
• Insert, change and delete operation supported.
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Result view• Spreadsheet like
result view.
• Tools for sorting and filtering data.
• Basic data analysis.
• Save molecular data in different formats.
Drug design environment – SOMA2
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Drug design environment – SOMA2
Result details• Visualisation of the
result molecules.
• Summary of computed properties.
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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