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