User:Eric Martz/Protein 3D Structure Resources for Educators 2016

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A Workshop for Educators at STCC
and other Springfield MA area colleges & schools.
by Eric Martz
Host: Dawn Tamarkin
1:00-5:00 PM, Monday and Tuesday, July 18 and 19, 2016
Springfield Technical Community College, 1 Armory Square, Springfield MA USA. Building 2, Room 614
Get here with STCC.MolviZ.Org



Introduction to Structural Bioinformatics and Genomics

  • Introduction to Structural Bioinformatics and Genomics
    • Why do we care about 3D macromolecular structure?
    • What are 3D structure data?
    • Where do 3D structure data come from?
    • How much 3D structure knowledge do we have?
    • What are the primary and derived 3D structure databases?

World Wide Protein Data Bank


  • UniProt.Org protein sequence database and a good place to find 3D models:
    • Click on the blue Sequences button (left side of page) to get the full length of the protein chain.
    • Click on the blue Structure button (left side of page):
      • Are there any PDB codes?
      • If yes: How much of the full length do they cover?
      • If no, click on the code after Protein Model Portal to look for homology models.
    • Detailed instructions: Practical Guide to Homology Modeling (includes how to look for empirical models before resorting to a homology model).

Major Jmol-Based Tools



  • A protein structure encyclopedia "wiki" with interactive molecular scenes in Jmol.
  • Green linked explanatory text changes the molecular scene.
  • Tutorials on specific molecules and definitions/explanations of structural biology terms and concepts.
  • Like Wikipedia, content is contributed by users.
  • Customization of molecular scenes is supported with straightforward Molecular Scene Authoring Tools. See Make Your Own Tutorials.
  • Unlike Wikipedia, authors are identified by their real names, hence receive credit and take responsibility.



  • A user-interface to Jmol that makes it much easier to see major structural features of macromolecules.
  • Used by Nature for its "3D" buttons in reports of new structures. Also by many other journals and bioinformatics resources.
  • Does not support customization of the molecular view. You are stuck with standard color schemes.
  • Easily saves static images or presentation-ready animations. Examples.
  • What Is It? More.

Lesson Plan with Assessment (3 afternoons)



Enolase (4enl; an enzyme in glycolysis) evolutionary conservation from ConSurf. Catalytic pocket is highly conserved.

Animations on this page were made using FirstGlance in Jmol.

Tutorials on Specific Macromolecules

  • In a computer lab, I like to hand out a short list of somewhat vague, open-ended questions to foster discussion in small groups of students. See Worksheets.
  • Most of these tutorials are in Proteopedia.Org, a wiki with user-authored content. Some articles are authored by students. As with Wikipedia, use your judgement. Unlike Wikipedia, authors' real names are at the bottom of each article and you can check their credentials by clicking on the names.

Molecules With Questions For Students (Java not needed)

Image:Lacrep anim small.gif

Molecules With No Questions ... Yet

No Java Needed


Potassium channel (1R3J) showing membrane surface planes (click Jmol at OPM).


Anti-Alzheimer's drug analog (*) interaction with Acetylcholinesterase (1gpk, cf. 1vot).

Tutorials requiring Java (fussy)

Getting Java to work with the unsigned applets in these older tutorials is too fussy for most students, but these could be shown in lectures.

  • At MolviZ.Org: Hemoglobin, Antibody, Major Histocompatibility Complex. A different approach than the ones in Proteopedia.

Molecule of the Month

These articles are authored by David S. Goodsell (The Scripps Research Institute and the RCSB PDB), a well-respected structural biologist.

Enzyme Reaction Videos

Make Your Own Tutorials

For Researchers

See Also

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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