SOMA2 - ChemAxon

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Transcript SOMA2 - ChemAxon

SOMA2 – Drug Design Environment

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.).

Drug design environment –

SOMA2

O H H H O H FROM MOLECULES … … TO PROTEINS … …AND CELL-LEVEL ACTIVITIES 

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

Drug design environment –

SOMA2

INTERNET, researcher’s PC a) CSC-network and computing grid Scientist interface,

SOMA2 environment

Basic technical concept

• WWW – interface is based on the XML – description of a program.

Dock to target protein GOLD on Linux Convert to 3D Corina on Solaris Calculate chemical properties Sybyl on Linux Query database ISIS on Solaris b) INPUT: • Different machine architectures are hidden.

• Automatic generation of program and platform specific configuration files.

SOMA2 environment O O 2D structure, known data O O CML • CML (chemical markup language) is used as internal data format (data transferred in XML).

• Unique computational workflows.

ADME prediction XML 2D > 3D conversion XML Docking XML OUTPUT: O • • • • • 2D structure, 3D structure, original data, docking score, ADME-values O

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

• • 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.

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.

Drug design environment –

SOMA2

Input molecules

• Upload files from local computer.

• Sketch molecules within the user interface.

Drug design environment –

SOMA2

Database query

• MDL ISIS host databases.

• Support for structure search.

• Search results imported to SOMA2 – system or downloaded.

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.

Drug design environment –

SOMA2

Workflow manager

• Free navigation between steps.

• Insert, change and delete operation supported.

Drug design environment –

SOMA2

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

Result details

• Visualisation of the result molecules.

• 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