The Molecular Level

Hand-On Workshops for High School Students
May 1, 2002

Introduction to Swiss-PdbViewer (Deep View)

Outline

1) Where Protein Models Come From

  1. X-ray Crystallography (Click HERE for slides.)
  2. NMR
  3. Homology Models

2) Introduction to Deep View

  1. Learn Deep View: Self Guiding Tutorial
  2. Deep View User Manual (or try this one)
  3. Get a protein-structure file from the Protein Data Bank:
    Cytochrome b5, PDB file code 1CYO.
    This is the file we will use in the Deep View Basic exercises, next.

3) Deep View Basic

  1. Windows and Help
  2. Manipulating the Model
  3. Selecting and Displaying
  4. Coloring
  5. Measuring and Labeling

4) Deep View Advanced

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

5) Discussion: What Can Modeling Do For You?

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 and then click Map Status: Download.
  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.
    Learn more about this discovery: Science, 289, #5486, 15 Sep 2000, pp. 1902-1906.

Additional Resources at The Molecular Level

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