Target audience: we assume that most or all of the educators at the workshop will be teaching at the College level (ages 18 and older). No specific target for High School / Secondary School.

A blueprint of topics that are mandatory for assessment within protein structure

Concept map (what to assess).


A systematic approach to assessment:

  1. List learning goals in terms of knowledge and skills.
  2. For each goal, write down a measurable outcome.
  3. Design a blueprint both for a written test and for a simulation test.
  4. Write items that test what the blueprint says we're testing.

Backwards design

This is a very natural technique, and yet, used by so few educators

  1. Evaluate what we specifically want the students to be able to do and to understand.
  2. What we can do to assess those.
  3. Assess the learning goals.

On a parallel description, when preparing a trip, you

  1. Decide where you want to go.
  2. Determine how you will know when you get to destination.
  3. Evaluate possible ways of performing the trip.

However, many (and that means a lot of) teachers are used to work the other way around:

  1. Write/design learning activities and learning materials.
  2. Define learning objectives and assessment points.

This is, they start by choosing the plane, boat or car before even knowing were to go.

Assessment vices and virtues

  • Bad and good practices in assessment. - Evaluating factual/memoristic knowledge vs. understanding and abilities.
  • How to assess abilities.
  • How to mark student's work out of the classroom.
  • Methods to motivate and involve the students.
  • Fostering student learning in off-campus activities and blended courses.
  • Designing assessment in the wrong order: choosing the plane, boat or car before even knowing were to go.

Strategies for teaching macromolecular structure-function relationships with interactive 3D visualization and assessment tools.

(Eric Martz)

A former version of this section is duplicated in the documentation pendrive (does not include the last sub-section)

Single class meeting in a computer lab:

  1. Class meeting follows a previous lecture on a specific molecule.
  2. Questions are handed out on paper.
  3. Students use an interactive 3D tutorial to help answer the questions. Working in pairs enhances learning for most (but not all) students.
  4. Encourage students to discuss with each other and the teacher: the discussion facilitates learning!
  5. Students hand in their answers.
  6. Answers are merely checked as received (learning has already taken place), or can be graded. This is not a test, but preparation for a conventional test.
  7. A conventional test may follow.

Interactive 3D tutorials that include Questions ready to use or adapt:

  1. DNA double helix structure: - Disponible también en español.
  2. Water: questions are in the Liquid Water section. Disponible también en español.
  3. Lac repressor complex with DNA operon.
  4. Major Histocompatibility Complex.

Longer course — multiple class meetings — student assignment:

  1. Each student chooses, or is assigned, a different molecule. See Browsing for a Molecule.
  2. Questions are assigned (suitable for any molecule). See Example Questions.
  3. Professor teaches one or several principles/methods. Each student applies these to their molecule.
  4. Students answer questions and prepare a report including snapshots of their molecule that answer each question. Powerpoint works well for such reports. Sample Student Report.
  5. Optionally, preliminary reports are emailed to the professor before the course is completed.
  6. Optionally, professor gives mid-course feedback on report to each student.
  7. Final reports are emailed and graded.

Easiest Yet Powerful Molecular Visualization

Full story: Top5.MolviZ.Org

  • Start at Proteopedia.Org
    • Name of molecule, published abstract, molecule in Jmol.
    • Full names of ligands (4mdh).
    • Evolutionary conservation (2vaa).
    • Popup for lectures.
    • Link out to FirstGlance in Jmol (used by Nature).
  • Continue in FirstGlance in Jmol
    • Main structural characteristics in one click each
    • Hide parts
    • Find components by name or sequence number/range
    • See non-covalent interactions, e.g. to ligand - examples:
      • 4mdh malate dehydrogenase with inhibitor in catalytic site
      • 1hxw HIV protease with inhibitor drug
      • 2vaa major histocompatibility with bound peptide ligand
      • 2hu4 influenza neuraminidase with Tamiflu drug bound (drug-resistant mutant)

See also Recent & Powerful Uses of Jmol.
See also Toobers,

Showing molecules with style: effective ways of presenting structure and Assessing Molecular Visualizations: Tools in the Molecular Workbench

(Frieda Reichsman)

This section is duplicated, with added links, in the documentation pendrive.


- students may not find these intuitive
spacefill, stick, ball and stick
backbone trace, backbone, detailed backbone
Transitions - building from backbones

Keeping Context - Importance of Orientation

fades at same zoom
transitions to zoomed detail (proteopedia automatic)
pauses are essential
scripts for transitions

Using colors effectively.

Sensible Coloring
standard color keys (DRUMS) Jmol, firstgance, PE, proteopedia,

* cpk
* charge
* sec str (Ras, chime, Jmol)
* N to C

Using Visibility Well

relationship of surface to eg cartoon
slabbing and cutaways

Electrostatic surfaces

uses of partial surfaces

Using Molecular Workbench for Assessment

Molecular models:
- Jmol
- 2D molecular dynamics

Question types
- OR
- MC/check answer
- Image/Annotation

Reporting options

Proteopedia: Teaching the Role of Structures on Biological Functions

(Jaime Prilusky, also Eric Martz)
See Teaching Strategies Using Proteopedia.

  • Description
  • Proteopedia compared to other resources
  • Brief tutorial
  • Using Proteopedia to quickly and easily do:
    • Making interactive 3D molecular scenes for projection in lectures
    • Preparing molecular structure tutorials for use by students
    • Using Proteopedia in student assignments
    • Proteopedia take-away: Export self contained Proteopedia pages for your portable computer or personal server.
    • Proteopedia Workbench, a user controlled access development area.