The Molecular Level

Hands-On Workshop
for
MERITS
(Maine Research Initiative for Teachers and Students)

Biological Molecular Modeling for Beginners

Suggested Reading

1. Any biochemistry textbook: Introductory chapters on protein structure.
2. How we know molecular structures: Chapters 2, 10, and 11, Crystallography Made Crystal Clear, Gale Rhodes, Academic Press, 2000. Available in the USM Library.
3. Molecular Modeling for Beginners, a tutorial introduction to Deep View.

Outline

1) Brief Introduction to Protein Structure

Click HERE for structure basics.

2) Where Protein Models Come From

(Click HERE for slides -- not all of these will be discussed in your workshop)

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

3) Introduction to Deep View

1. GET and 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. We will usethis file for 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

• Protein Data Bank: Experimental Models (Crystallographic and NMR)
• SWISS-MODEL: Homology Models

Examples: Judging Model Quality

1. Homology Model Project: Modeling a Humanized Mouse Antibody
2. 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).
3. NMR Model:
   Anti-digoxin antibody 26-10, Vl domain, 15 models: 1MAJ.
   Learn more about this model.

Suggested Reading

1. Any biochemistry textbook: Introductory chapters on protein structure.
2. How we know molecular structures: Chapters 2, 10, and 11, Crystallography Made Crystal Clear, Gale Rhodes, Academic Press, 2000. Provided to workshop participants.

Additional Resources at The Molecular Level

To Molecular Level

To Gale Rhodes Home