1. Overview of the Event 2. This Year's Theme 3. Building Your Models

Building Your Physical Protein Models

The final step to successfully competing in the Science Olympiad Protein Modeling Event is to actually build your protein models. This section will cover how to construct a protein model, including information on:

The Visualization Environment

Overall Layout of the Visualization Environment

Changing the Display Format and Color Schemes

Using the Select and Restrict Commands

Advanced Jmol Training Guide

For students that really want to push their understanding and knowledge of Jmol further, the advanced Jmol training web pages below will provide a more detailed review of commands and techniques for manipulating protein and DNA structures in the Jmol visualization environment.

Folding a Mini-Toober Model

Every team competing in the Science Olympiad Protein Modeling Event will be expected to create a pre-build protein model of specific protein structure. The pre-build model will be created using a purchased "pre-build" Mini-Toober kit from www.3dmoleculardesigns.com, or with found materials of the participants' choosing such as KwikTwist tie-down ropes.

The same pre-build model will be used at each level of the competition (invitational, regional, state and national). Participants will take their pre-build model home after each event.

The pre-build model must be impounded prior to the beginning of the event (usually the morning of the event. The pre-build model should be submitted with a 4"x6" card with a written description of the model's colors and creative additions, addressing what, how, and why. Check the official rules for details

This section contains three important video tutorials describing how to map out and fold these models.

Mapping Out the Mini-Toober Model

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Folding Secondary Structures

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Folding the 3-D Shape

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A Note on the Length of Your Toober

An astute student may notice that the length of the Toober included in a prebuild modeling kit purchased from 3D Molecular Designs appears to be one amino acid length (2cm) too short. For example, if you are modeling amino acids 1-85, you would expect the length of Toober to be 170cm long (at a scale of 1 amino acid = 2cm) - but it is actually 168cm long.

The video below attempts to explain this apparent discrepancy using schematic graphics and Jmol renderings.

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Taking your model further and judging tips

Pre-build models are expected to have additional added features and all models will undergo a judging process. This section contains two important video tutorials describing how to approach adding additional features on the pre-build model and how models will be judged.

Going Beyond Just the Backbone

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How do you know which residues are important?

The protein that you are modeling may be large and complex. Here are a few simple ways to figure out which amino acid residues in the structure are important for its structure or function:

Judging the Protein Models

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Zinc Finger Example Model

The CBM's Zinc Finger Folding Kit works as an example modeling activity for the Science Olympiad Protein Modeling Event. The model is available to borrow free from the CBM Lending Library, and can be used alongside the online Zinc Finger Design Environment.

Also available are example Scoring Rubrics and Scoring Spreadsheets for this zinc finger activity, which mimic the rubrics and scoresheets used by event supervisors in the Science Olympiad Protein Modeling Event.

Exploring the RCSB Protein Databank for the Onsite Jmol Exploration

This year, instead of modeling a protein during the on-site competition, teams will answer questions as part of a "Jmol Exploration".

The purpose of the Jmol exploration component of this year’s event is to allow students to demonstrate their skill in using Jmol to manipulate and explore a pdb file, and navigate the RCSB Protein Data Bank website (www.rcsb.org).

The video below will describe the RCSB Protein Databank Website, and the features teams should be familiar with for the onsite "Jmol Exploration" portion of the competition.

Science Olympiad

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