Ideas for Lessons Employing 3D Molecular Visualization
Illustrating Lectures
Existing tutorials, or any molecule loaded into the Protein Explorer, can serve to illustrate lectures. Students can review the illustrations at home, or in computer labs.

If you show arbitrary molecules loaded into the Protein Explorer, you can make a web page of links for your class which brings up these molecules.

When illustrating lectures, Don't forget to move your molecules early and often! You may be familiar with the 3D structure of the molecule you are showing, but it is all new to your students. Forgetting to move the structure often enough is a common pedagogic mistake -- it makes the molecule go "flat". The students can't see its 3D structure without rotation.

Each segment of your molecular visualization presentation should answer a question. The question and the answer should be explicitly stated.

Questions on Paper
Hand out questions on paper, and assign your students to answer them while viewing a particular tutorial. This can be done during a scheduled computer lab, or as homework. The questions give the students focus and a defined and limited set of goals while going through the tutorial images. Sets of questions, ready to print and hand out, are provided with the tutorials on Antibody and Major Histocompatibility Complex. If you write such questions for another tutorial, please email them to me so they can be posted here.

Amino Acid Quizzer
Assign each student or group a sequence number, or range of numbers, and ask them to identify the corresponding amino acids using the Amino Acid Quizzer. Ask them to tell whether the amino acid(s) are hydrophobic, polar, or charged, and which are at the amino and carboxy termini.

Structure Analysis
Assign your students to explore a molecule in the Protein Explorer. Ask them to write a description of the secondary structure, distribution of hydrophobic sidechains, active site, or other features you have covered in class. Optionally, have each student or group show their molecule to the class.

Sequence to Structure
Assign each student or group a short nucleotide sequence. Ask them to translate it to the amino acid sequence, then use GenBank to find the protein containing this sequence. Then ask them to view the 3D structure of this protein, describe where in the 3D structure the sequence segment fits, and the function of that segment. (Contributed by Gary Harris, Wellesley College, Wellesley MA.)

A ready-to-assign exercise is offered by Charles Sackerson, Iona College, New Rochelle NY. A sequence is given, with instructions for finding the molecule with BLAST. Next, using BLASTX, the six possible translated amino acid sequences are obtained and matching proteins are listed. Disease associations are noted. The molecule is then searched for at the PDB, and the 3D structure viewed in Chime.

Feedback to Eric Martz.