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Protein modeling with discovery studio

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Introduction to Discovery Studio as part of the hands on Demonstration organized at Structural Bioinformatics Laboratory, Åbo Akademi University. The tutorials are available upon request.

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Protein modeling with discovery studio

  1. 1. 12.10.2010Kisun Pokharel
  2. 2. Command menusToolbars ProtocolsHierarchyviewGraphics WindowProtocols explorerTable view Jobs explorer
  3. 3.  File menu: commands for tasks such as opening files, saving files, printing, and viewing file properties Edit menu: Commands for tasks such as selecting, copying, pasting, and setting preferences View menu: Commands for tasks such as changing the way objects appear in various views and for choosing which views should be shown or hidden Chemistry menu: Commands for taksks that modifythe chemical make up of the molecules Structure menu: commands for tasks such as adding or removing labels, calculating solvent accessibility, cleaning up geometry, adding surface charges and superimposing multiple molecules Sequence menu: commands to manage protein sequences and protein sequence alignments Chart menu: commands to create modify adifferent plot types Script menu: commands that run scripts for visualization, slection, structure editing, and ligand interactions Window: Commands that allow you to control the display of open windows Help: Commands to access the Discovery studio help system and the accelerys website.
  4. 4.  Shortcuts to menu commands Add or hide toolbars from View|Toolbars
  5. 5.  Contain methods that perform quick operations on selected objects and are usually performed locally, as opposed to protocols which are always sent to the server for processing. Tools panel can be made visible from view|Explorers|tools
  6. 6.  Advanced modeling and analysis tasks that are computed by DS server Protocols panel can be visualized from: View|Explorers|Protocols
  7. 7.  TO browse files created by discovery studio and the files in hard drive
  8. 8.  For selecting atoms, amino acids or molecules Selections can be made for 3D- view, Data table and the sequence window too. The hierarchy panel is opened from view|Hierarchy
  9. 9.  Shows data and values associated to the molecular structure The data can be viewed, modified and sorted in the data table Value in gray background can’t be modified Open data table by View|Data table
  10. 10.  NO WWW or printed tutorials Built-in extensive tutorials and help system Can be browsed fromHelp|Help Topics/Getting Started/Tutorials

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