The Molecular Level

Hands-On Workshops

Introduction to Deep View (Swiss-PdbViewer)

Typical Outline and Resources

Assignment

Please study these materials before coming to the workshop.

  1. Chapters 2, 10, and 11, Crystallography Made Crystal Clear, Gale Rhodes, Academic Press, 2000.
    This reading is available on the stand outside my office door -- my office is inside Science lab 366.
  2. Deep View Tutorial: Molecular Modeling for Beginners

Outline

1) Brief Introduction to Protein Structure

2) Where Protein Models Come From

(Click HERE for slides)

  1. X-ray Crystallography
  2. NMR
  3. Homology Models

3) Introduction to Deep View

  1. Learn Deep View: Self Guiding Tutorial
  2. Deep View User Manual (If not posted yet, try HERE)
  3. Get a protein-structure file from the Protein Data Bank:
    Cytochrome b5, PDB file code 1CYO OR major histocompatibility complex, PDB file code 1HHI.
  4. We will use one of these files for Deep View Basic exercises, next.

4) Deep View Basic

  1. Windows and Help
  2. Manipulating the Model
  3. Selecting and Displaying (from menus)
  4. Coloring
  5. Measuring and Labeling
  6. Using the Control Panel
  7. Making Pretty Pictures

5) Deep View Advanced

  1. Surfaces
  2. Comparing Models
  3. Homology Modeling
  4. Judging Model Quality

Resources

Get Deep View

Learn to View in Stereo

Get Protein Models

Examples: Project File of Fab Structures

Contains the full set of antibody structures presented and compared in this demonstration.

See Structural Insights into the Evolution of an Antibody Combining Site, G. J. Wedemayer, P. A. Patten, L. H. Wang, P. G. Schultz, R. C. Stevens (USM Chemistry, class of 1986), Science 1997 June 13; 276 (5319):1665.

Raw antibody models used in this demonstration (direct from PDB):

  1. Germline antibody: 2RCS
  2. Germline antibody plus hapten: 1AJ7
  3. Mature antibody: 1HKL
  4. Mature antibody plus hapten: 1GAF

Examples: Judging Model Quality

  1. Crystallographic Model:
    Electron density map of 1AJ7: Click HERE. The map file will appear as gibberish in your browser. After it has downloaded completely, choose File: Save As... choose Source format, and save the file to your desktop. You can open this file in Deep View (after first opening 1AJ7) using File: Open Electron Density Map: DN6.
    If the map file does not show up among available files, you'll need to associate it with Deep View (Windows), or change its type to BINA and its creator to hDmp, using a program like FileTyper (Macintosh).
  2. NMR Model:
    Anti-digoxin antibody 26-10, Vl domain, 15 models: 1MAJ.
    Learn more about this model.
  3. Homology Model and Templates
    Sequence of newly discovered proteorhodopsin (text file in FASTA format): Click here. (If you see the file in a browser window, save as text file.)
    Bacteriorhodopsin, 1C3W, a good template for modeling proteorhodopsin.
    Click here for a homology model of proteorhodopsin (1C3W as template), optimized by Swiss-Model. This model contains retinal in the same position as in the template.
    Learn more about this discovery: Science, 289, #5486, 15 Sep 2000, pp. 1902-1906.
  4. Project: Modeling a Humanized Mouse Antibody

Additional Resources at The Molecular Level

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