User:Wayne Decatur/NASCE2011

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General Introduction

  • Thanks to the organizers of the NASCE2011
  • About me
  • Overview of the workshop planned
  • Gauge Audience, Adjust plan?

Introduction to Proteopedia

Under the Hood

  • Wiki implementation, very specialized
    • references
      • Create a page for example with references
    • other technical aspects related to Jmol and other media
  • Jmol


The Structure Data

Protein Data Bank


  • Proteopedia - interactive 3D encylopedia of macromolecular structures and structural biology resources to which scientists contribute and use to share structural biology content
  • Help:Getting Started in Proteopedia
  • User or Sandbox login
  • We encourage you all to become users of any sort. If you become a registered user, you can save information in your userspace regardless of your overall contribution to public spaces.

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 (nearly 75,000) with interactive scene links and links to useful resources
    • Example 1p3v (PDB 4 digit alphanumeric accession number)
      • Evolutionary conservation - conserved patches are good candidates for functional sites: see explanation and caveat, and see also The ConSurf Database and The ConSurf Server Other examples: 4enl or 5cyt
        • Show how to use ConSurf Server - Be sure to choose to "Let me select the sequences for the analysis manually out of Blast results"

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
  • Under adoptions on main page , there is Orientations of Proteins in Membranes (OPM) database from the University of Michigan (Ann Arbor, Michigan, USA), and knowing the spatial arrangement of protein with respect to the hydrocarbon core of the lipid bilayer and other details of topology could be useful for understanding the function of several proteins involved in endocrinology, example 2rh1

Structural Biology for Non-structural Biologists

  • MolviZ "Top 5" by Eric Martz
  • Polyview-3D = fancy PyMol views and animations made super easy via a web server with forms.
    • Example for 2rh1
      • Use overall structure with ligands off; under chain and color rendering chain a as cartoon and hide remaining; under individual residue highlight enter a:408:cf,a:290:ms from converter
      • 2rh1 from Polyview-3D (probably the gap in the cartoon is an artifact due to the way the numbering is for 2rh1 due to the chimeric nature of the receptor with lysozyme (see PDBSum
    • Makes animations too and/or morphs as well using a file with multiple models

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 PubMed, PMID all that is needed for references in text, combined with a reference list at end
  • Proteopedia:How to Make a Page
  • How to edit pages in Proteopedia
  • Special:Upload List of allowed file types: png, jpg, jpeg, tiff, tif, gif, mgif, pdb, cif, mmcif, cml, mol, xyz, kin, mmol
  • To do:
    • Try making a sandbox page
    • Add a subject or title to your page
    • Insert a 3D structure window on your page

Proteopedia Scene Authoring and Adding Green Scene Links to a Page

  • Proteopedia's Scene Authoring Tools
  • To do:
    • Load a structure 3ciy or previous scene
    • Set your scene. Undo/Redo features.
  • Save your scene
    • Try it out and then add and improve. Repeat until you are happy with result.
  • Add the scene to the page you made by pasting the text from the scene text box into the page editing box.
    • Return to scene authoring tools to make more scenes or improve the one you have.
    • If you update a scene, change the text on the page to designate playing of the new scene.

Time or need permitting

  • Assessing structure
  • Can't find an empirical 3D model for your sequence?
    • Use the sequence of your protein to search the Structural Genomics Target Database for crystal structures nearing publication.
    • Endeavor to generate a theoretical model by one of various means


Macromolecular Visualization

Small Molecule Visualization and Model Kits

Topic Pages - Education

Authoring Scenes and Views in Proteopedia and beyond



  1. B. Bienfait and P. Ertl, JSME: a free molecule editor in JavaScript, Journal of Cheminformatics 5:24 (2013) article

Class Sandboxes

Sandbox Reserved 171 Sandbox Reserved 181
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Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur

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