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Dynamic web application for drug design research M. Chapman 1 , N. MacCuish 1 , J. MacCuish 1

Dynamic web application for drug design research M. Chapman 1 , N. MacCuish 1 , J. MacCuish 1 J. Bradley 2 , J. Blankley 3 1 Mesa Analytics & Computing, Inc., Santa Fe, New Mexico, USA 2 Drexel University, Philadelphia, PA, USA 3 Pfizer (retired), Ann Arbor, MI, USA. ABSTRACT.

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Dynamic web application for drug design research M. Chapman 1 , N. MacCuish 1 , J. MacCuish 1

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  1. Dynamic web application for drug design research M. Chapman1, N. MacCuish1, J. MacCuish1 J. Bradley2, J.Blankley3 1Mesa Analytics & Computing, Inc., Santa Fe, New Mexico, USA 2Drexel University, Philadelphia, PA, USA 3Pfizer (retired), Ann Arbor, MI, USA

  2. ABSTRACT The dynamic Web application, WebFlowDD, introduces synthetic organic chemistry students to the world of drug design through a pharmaceutical industry workflow. Students and researchers have access to simple tasks that are commonplace in an industrial setting and have the opportunity to run a variety of freeware and Web-services as they tackle synthetic challenges in drug design. This poster focuses on WebFlowDD combined with Cheminformatics Virtual Classroom (ChemVC), an e-Learning environment for students to learn specific topics in drug discovery.

  3. WebflowDD Interface

  4. WebflowDD Interface • Dashboard design with four expandable, dynamically interactive panels • Data panel allows for import and management of data for the various tasks outlined in the Task panel • View panel updates with views for any data imported from the Data window or visualization dynamically generated from interaction with the Task panel • Task panel allows users to choose specific workflows of interest and leads them through a workflow • Analysis panel enables users to interact with Tasks that involve intermediate steps.

  5. Dashboard Design

  6. WebFlowDD Tasks • Similarity Searching • Visualize Common Substructures (ChemTattooTM) • Build QSAR Models • Make predictions with pre-computed models (internal or via web services)

  7. Database Similarity Searching SMILES can be pasted in as queries for Similarity Searching on databases local to the WebFlowDD server as well as hits can be used to interface with ChemSpider or other on-line database services.

  8. Interface to ChemSpider http://www.chemspider.com/

  9. Interface to Webservice Modeling QSAR Models from a webservice provided by R. Guha at Indiana University, enables users to generate a spectrum of QSAR Models from their imported data. Models are built and results displayed in the View panel.

  10. Predictive Modeling • QSAR models, solubility models, etc. are created with computed parameters from CDK • Pre-computed models are menu available for predictions on new data sets

  11. Predictive Modeling Example Predictive Modeling workflow. Users chose a parameter set to build a model. A SMILES is uploaded and a prediction generated from the pre-computed model.

  12. Lessons on www.chemvc.com Users requiring more background for workflow tasks, can look to ChemVC for related subject matter.

  13. Acknowledgements • WebFlowDD is written in Python, Jython, Java and C++. It relies on several 3rd party Free/Open Source Software (FOSS) packages: • CDK -- the Chemistry Development Kit provides chemical properties and 2D depiction coordinates • CherryPy -- WebFlowDD is built atop this web application framework • Elixir -- an Object-Relational Mapper layer that sits atop SQLAlchemy • excanvas -- provides Internet Explorer with support for the HTML5 Canvas Tag • flot -- a JavaScript-based graphing package • Jinja - HTML templating engine used by WebFlowDD • jQuery and jQuery UI -- JavaScript libraries that help make WebFlowDD pages interactive • jQuery clickMenu plugin -- provides pulldown menus in the Data pane • jQuery Dimensions plugin -- manages the geometry of the web page elements • jQuery spin btn plugin -- turns text fields into numeric spin boxes • OpenBabel -- providing underlying support for chemical fingerprinter and ChemTattoo • Simplejson -- used on the server side to convert Python data structures to and from JSON (JavaScript Object Notation) for exchange with web browsers • SOAPy -- WebFlowDD uses SOAP to communicate with some other web services • SQLAlchemy -- provides a database abstraction layer • SQLite3 -- providing persistent store for WebFlowDD • Other underlying FOSS packages: Beaker, fpconst, Imaging, numpy, python-datautil, pytz • Consultants Webservices: Indiana University: R. Guha, ChemSpider • David Moreland

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