1. Visually Demonstrating the Principles of Protein Folding Bill McClung, Jeff Schwehm, Greg Wolffe

2. Teaching About Molecules Molecules are complicated 3D objects. We use 2D representations that are difficult for students to visualize in 3D. 3D visualization tools help convey the story about these molecules.

3. Simple Ways To Think About Protein Folding Primary Sequence Secondary Structure Tertiary Structure Quaternary Structure FLWKDQI

4. Biochemical Properties Involved in Protein or Peptide Folding Hydrophobicity Hydrophilicity Like Interacts with Like Secondary Structure Propensities of the Amino Acids

5. Developing the Model Each amino acid has empirically determined values of properties. Mathematical model uses amino acid sequences and these values to predict secondary structure. The model produces coordinates that represent this secondary structure.

6. Generating the Visualization Model output is used to create an interactive 3D ribbon diagram of the molecule. Cross-platform Technology C/C++, Perl OpenGL

7. Instructor Usage Not to accurately predict protein folding. To demonstrate the principles of secondary structure formation. Used as a bridge to “real, industrial strength” tools. (PDB tools) Targeted for high school students and lower level undergraduates. Courses: Biology, Chemistry, Biochemistry and General Science.

8. Student Usage Can select and/or modify amino acid sequences to develop an intuition of the resulting 3D structure. Can change the weighting of properties such as hydrophobicity or propensities to develop a deeper understanding of the effect of these properties on folding behavior.