User:Wayne Decatur/UNH Seminar Feb 1st 2011

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  • Overview of the talk
    • My Recent Research
    • Cursory coverage of several free (and mainly open-source) options for molecular visualization

Yeast snoRNAs

  • Introduction to snoRNAs - most modify and are not-essential to yeast
  • Nobel prizes 2009 studies of the structure and function of the ribosome structure
    • Jmol
      • The Application
      • The Java Applet - Demonstration
    • Locations of the modifications in the context of the functional ribosome
    • Yeast snoRNA database
    • Turns out of you remove clusters of modifications or modifications at critical locations and examine processing of pre-rRNA and properties of mature ribosome, find effects.


Protein Data Bank


Types of Proteopedia pages

Topic Pages

User Pages

  • Other users cannot edit pages in this space

PDB Entry Pages

  • Proteopedia has an entry for every PDB entry (over 70,000) with interactive scene links and links to useful resources

FirstGlance in Jmol

  • Views and Convenience buttons
    • How many chains? - Use 3pla
    • Key Resources:
      • Biological Unit
      • Missing pieces?; PDBsum link on Proteopedia entry pages helpful for this as well

Structural Biology for Non-structural Biologists

Proteopedia Page Authoring

  • Model of a wiki
  • Sandbox - there is a "student" login that can be used by groups for editing these for teaching purposes
  • Conveniences
    • Buttons for 3D structure windows and other commonly used items
    • Since a large amount of references are from Pub-Med, PMID all that is needed for references
  • Help:Getting Started in Proteopedia

Proteopedia Scene Authoring

  • Scene Authoring Tools
    • Load a structure 2zi0 or previous scene
    • Set your scene. Undo/Redo features.
    • Save your scene
    • Add the scene to the page
  • Try it out and then add and improve. Repeat.


  • closing slides


Time permitting


Macromolecular Visualization

Small Molecule Visualization and Model Kits

Topic Pages - Education

Authoring Scenes and Views in Proteopedia and beyond


Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur

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